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"index": 1, "num_nts": 9, "nts_short": "UUGAUCCUG", "nts_long": "///2/8,///2/9,///2/10,///2/11,///2/12,///2/13,///2/14,///2/15,///2/16" } ] }, { "index": 2, "type": "hairpin loop", "bridging_nts": [ 10 ], "stem_indices": [ 10 ], "summary": "[1] 10 [2.69 2.80] 2", "num_nts": 12, "nts_short": "CGGCCGGUACAG", "nts_long": "///2/69,///2/70,///2/71,///2/72,///2/73,///2/74,///2/75,///2/76,///2/77,///2/78,///2/79,///2/80", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 10, "nts_short": "GGCCGGUACA", "nts_long": "///2/70,///2/71,///2/72,///2/73,///2/74,///2/75,///2/76,///2/77,///2/78,///2/79" } ] }, { "index": 3, "type": "hairpin loop", "bridging_nts": [ 5 ], "stem_indices": [ 17 ], "summary": "[1] 5 [2.156 2.162] 3", "num_nts": 7, "nts_short": "GUAAUUC", "nts_long": "///2/156,///2/157,///2/158,///2/159,///2/160,///2/161,///2/162", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "UAAUU", "nts_long": "///2/157,///2/158,///2/159,///2/160,///2/161" } ] }, { "index": 4, "type": "hairpin loop", "bridging_nts": [ 6 ], "stem_indices": [ 19 ], "summary": "[1] 6 [2.196 2.203] 5", "num_nts": 8, "nts_short": "CUUCGCGG", "nts_long": "///2/196,///2/197,///2/198,///2/199,///2/200,///2/201,///2/202,///2/203", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "UUCGCG", "nts_long": "///2/197,///2/198,///2/199,///2/200,///2/201,///2/202" } ] }, { "index": 5, "type": "hairpin loop", "bridging_nts": [ 6 ], "stem_indices": [ -11 ], "summary": "[1] 6 [2.288 2.295] 1", "num_nts": 8, "nts_short": "GGUGACUC", "nts_long": "///2/288,///2/289,///2/290,///2/291,///2/292,///2/293,///2/294,///2/295", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "GUGACU", "nts_long": "///2/289,///2/290,///2/291,///2/292,///2/293,///2/294" } ] }, { "index": 6, "type": "hairpin loop", "bridging_nts": [ 9 ], "stem_indices": [ 24 ], "summary": "[1] 9 [2.377 2.387] 7", "num_nts": 11, "nts_short": "GUCGCCGUGCC", "nts_long": "///2/377,///2/378,///2/379,///2/380,///2/381,///2/382,///2/383,///2/384,///2/385,///2/386,///2/387", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 9, "nts_short": "UCGCCGUGC", "nts_long": "///2/378,///2/379,///2/380,///2/381,///2/382,///2/383,///2/384,///2/385,///2/386" } ] }, { "index": 7, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 26 ], "summary": "[1] 4 [2.416 2.421] 4", "num_nts": 6, "nts_short": "UCAGGG", "nts_long": "///2/416,///2/417,///2/418,///2/419,///2/420,///2/421", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "CAGG", "nts_long": "///2/417,///2/418,///2/419,///2/420" } ] }, { "index": 8, "type": "hairpin loop", "bridging_nts": [ 10 ], "stem_indices": [ 28 ], "summary": "[1] 10 [2.441 2.452] 3", "num_nts": 12, "nts_short": "CCUGAGAAACGG", "nts_long": "///2/441,///2/442,///2/443,///2/444,///2/445,///2/446,///2/447,///2/448,///2/449,///2/450,///2/451,///2/452", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 10, "nts_short": "CUGAGAAACG", "nts_long": "///2/442,///2/443,///2/444,///2/445,///2/446,///2/447,///2/448,///2/449,///2/450,///2/451" } ] }, { "index": 9, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 29 ], "summary": "[1] 4 [2.462 2.467] 2", "num_nts": 6, "nts_short": "CCAAGG", "nts_long": "///2/462,///2/463,///2/464,///2/465,///2/466,///2/467", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "CAAG", "nts_long": "///2/463,///2/464,///2/465,///2/466" } ] }, { "index": 10, "type": "hairpin loop", "bridging_nts": [ 5 ], "stem_indices": [ 31 ], "summary": "[1] 5 [2.498 2.504] 3", "num_nts": 7, "nts_short": "CGACCCG", "nts_long": "///2/498,///2/499,///2/500,///2/501,///2/502,///2/503,///2/504", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "GACCC", "nts_long": "///2/499,///2/500,///2/501,///2/502,///2/503" } ] }, { "index": 11, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 34 ], "summary": "[1] 4 [2.539 2.544] 2", "num_nts": 6, "nts_short": "CUUUCG", "nts_long": "///2/539,///2/540,///2/541,///2/542,///2/543,///2/544", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "UUUC", "nts_long": "///2/540,///2/541,///2/542,///2/543" } ] }, { "index": 12, "type": "hairpin loop", "bridging_nts": [ 11 ], "stem_indices": [ -18 ], "summary": "[1] 11 [2.569 2.581] 1", "num_nts": 13, "nts_short": "ACUUUAAAUCCUU", "nts_long": "///2/569,///2/570,///2/571,///2/572,///2/573,///2/574,///2/575,///2/576,///2/577,///2/578,///2/579,///2/580,///2/581", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 11, "nts_short": "CUUUAAAUCCU", "nts_long": "///2/570,///2/571,///2/572,///2/573,///2/574,///2/575,///2/576,///2/577,///2/578,///2/579,///2/580" } ] }, { "index": 13, "type": "hairpin loop", "bridging_nts": [ 19 ], "stem_indices": [ 37 ], "summary": "[1] 19 [2.601 2.621] 2", "num_nts": 21, "nts_short": "GGCAAGUCUGGUGCCAGCAGC", "nts_long": "///2/601,///2/602,///2/603,///2/604,///2/605,///2/606,///2/607,///2/608,///2/609,///2/610,///2/611,///2/612,///2/613,///2/614,///2/615,///2/616,///2/617,///2/618,///2/619,///2/620,///2/621", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 19, "nts_short": "GCAAGUCUGGUGCCAGCAG", "nts_long": "///2/602,///2/603,///2/604,///2/605,///2/606,///2/607,///2/608,///2/609,///2/610,///2/611,///2/612,///2/613,///2/614,///2/615,///2/616,///2/617,///2/618,///2/619,///2/620" } ] }, { "index": 14, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 39 ], "summary": "[1] 4 [2.618 2.623] 2", "num_nts": 6, "nts_short": "CAGCCG", "nts_long": "///2/618,///2/619,///2/620,///2/621,///2/622,///2/623", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "AGCC", "nts_long": "///2/619,///2/620,///2/621,///2/622" } ] }, { "index": 15, "type": "hairpin loop", "bridging_nts": [ 7 ], "stem_indices": [ 46 ], "summary": "[1] 7 [2.820 2.828] 2", "num_nts": 9, "nts_short": "UGUUCAAAG", "nts_long": "///2/820,///2/821,///2/822,///2/823,///2/824,///2/825,///2/826,///2/827,///2/828", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 7, "nts_short": "GUUCAAA", "nts_long": "///2/821,///2/822,///2/823,///2/824,///2/825,///2/826,///2/827" } ] }, { "index": 16, "type": "hairpin loop", "bridging_nts": [ 20 ], "stem_indices": [ -27 ], "summary": "[1] 20 [2.882 2.903] 1", "num_nts": 22, "nts_short": "UUCUAUUUUGUUGGUUUUCGGA", "nts_long": "///2/882,///2/883,///2/884,///2/885,///2/886,///2/887,///2/888,///2/889,///2/890,///2/891,///2/892,///2/893,///2/894,///2/895,///2/896,///2/897,///2/898,///2/899,///2/900,///2/901,///2/902,///2/903", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 20, "nts_short": "UCUAUUUUGUUGGUUUUCGG", "nts_long": "///2/883,///2/884,///2/885,///2/886,///2/887,///2/888,///2/889,///2/890,///2/891,///2/892,///2/893,///2/894,///2/895,///2/896,///2/897,///2/898,///2/899,///2/900,///2/901,///2/902" } ] }, { "index": 17, "type": "hairpin loop", "bridging_nts": [ 8 ], "stem_indices": [ 54 ], "summary": "[1] 8 [2.957 2.966] 2", "num_nts": 10, "nts_short": "AGGUGAAAUU", "nts_long": "///2/957,///2/958,///2/959,///2/960,///2/961,///2/962,///2/963,///2/964,///2/965,///2/966", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 8, "nts_short": "GGUGAAAU", "nts_long": "///2/958,///2/959,///2/960,///2/961,///2/962,///2/963,///2/964,///2/965" } ] }, { "index": 18, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 55 ], "summary": "[1] 4 [2.994 2.999] 2", "num_nts": 6, "nts_short": "CGAAAG", "nts_long": "///2/994,///2/995,///2/996,///2/997,///2/998,///2/999", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GAAA", "nts_long": "///2/995,///2/996,///2/997,///2/998" } ] }, { "index": 19, "type": "hairpin loop", "bridging_nts": [ 9 ], "stem_indices": [ 57 ], "summary": "[1] 9 [2.1054 2.1064] 4", "num_nts": 11, "nts_short": "GAUCAGAUACC", "nts_long": "///2/1054,///2/1055,///2/1056,///2/1057,///2/1058,///2/1059,///2/1060,///2/1061,///2/1062,///2/1063,///2/1064", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 9, "nts_short": "AUCAGAUAC", "nts_long": "///2/1055,///2/1056,///2/1057,///2/1058,///2/1059,///2/1060,///2/1061,///2/1062,///2/1063" } ] }, { "index": 20, "type": "hairpin loop", "bridging_nts": [ 6 ], "stem_indices": [ 62 ], "summary": "[1] 6 [2.1113 2.1120] 4", "num_nts": 8, "nts_short": "AUUCCCAU", "nts_long": "///2/1113,///2/1114,///2/1115,///2/1116,///2/1117,///2/1118,///2/1119,///2/1120", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "UUCCCA", "nts_long": "///2/1114,///2/1115,///2/1116,///2/1117,///2/1118,///2/1119" } ] }, { "index": 21, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 63 ], "summary": "[1] 4 [2.1141 2.1146] 2", "num_nts": 6, "nts_short": "GGAAAC", "nts_long": "///2/1141,///2/1142,///2/1143,///2/1144,///2/1145,///2/1146", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GAAA", "nts_long": "///2/1142,///2/1143,///2/1144,///2/1145" } ] }, { "index": 22, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 65 ], "summary": "[1] 4 [2.1178 2.1183] 4", "num_nts": 6, "nts_short": "UGCAAA", "nts_long": "///2/1178,///2/1179,///2/1180,///2/1181,///2/1182,///2/1183", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GCAA", "nts_long": "///2/1179,///2/1180,///2/1181,///2/1182" } ] }, { "index": 23, "type": "hairpin loop", "bridging_nts": [ 8 ], "stem_indices": [ 71 ], "summary": "[1] 8 [2.1245 2.1254] 2", "num_nts": 10, "nts_short": "GACUCAACAC", "nts_long": "///2/1245,///2/1246,///2/1247,///2/1248,///2/1249,///2/1250,///2/1251,///2/1252,///2/1253,///2/1254", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 8, "nts_short": "ACUCAACA", "nts_long": "///2/1246,///2/1247,///2/1248,///2/1249,///2/1250,///2/1251,///2/1252,///2/1253" } ] }, { "index": 24, "type": "hairpin loop", "bridging_nts": [ 1 ], "stem_indices": [ -36 ], "summary": "[1] 1 [2.1269 2.1271] 1", "num_nts": 3, "nts_short": "GGC", "nts_long": "///2/1269,///2/1270,///2/1271", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///2/1270" } ] }, { "index": 25, "type": "hairpin loop", "bridging_nts": [ 34 ], "stem_indices": [ 72 ], "summary": "[1] 34 [2.1281 2.1316] 3", "num_nts": 36, "nts_short": "GACAGGAUUGACAGAUUGAUAGCUCUUUCUCGAUUC", "nts_long": "///2/1281,///2/1282,///2/1283,///2/1284,///2/1285,///2/1286,///2/1287,///2/1288,///2/1289,///2/1290,///2/1291,///2/1292,///2/1293,///2/1294,///2/1295,///2/1296,///2/1297,///2/1298,///2/1299,///2/1300,///2/1301,///2/1302,///2/1303,///2/1304,///2/1305,///2/1306,///2/1307,///2/1308,///2/1309,///2/1310,///2/1311,///2/1312,///2/1313,///2/1314,///2/1315,///2/1316", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 34, "nts_short": "ACAGGAUUGACAGAUUGAUAGCUCUUUCUCGAUU", "nts_long": "///2/1282,///2/1283,///2/1284,///2/1285,///2/1286,///2/1287,///2/1288,///2/1289,///2/1290,///2/1291,///2/1292,///2/1293,///2/1294,///2/1295,///2/1296,///2/1297,///2/1298,///2/1299,///2/1300,///2/1301,///2/1302,///2/1303,///2/1304,///2/1305,///2/1306,///2/1307,///2/1308,///2/1309,///2/1310,///2/1311,///2/1312,///2/1313,///2/1314,///2/1315" } ] }, { "index": 26, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 75 ], "summary": "[1] 4 [2.1353 2.1358] 3", "num_nts": 6, "nts_short": "AGCGAU", "nts_long": "///2/1353,///2/1354,///2/1355,///2/1356,///2/1357,///2/1358", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GCGA", "nts_long": "///2/1354,///2/1355,///2/1356,///2/1357" } ] }, { "index": 27, "type": "hairpin loop", "bridging_nts": [ 6 ], "stem_indices": [ 76 ], "summary": "[1] 6 [2.1366 2.1373] 2", "num_nts": 8, "nts_short": "GUUAAUUC", "nts_long": "///2/1366,///2/1367,///2/1368,///2/1369,///2/1370,///2/1371,///2/1372,///2/1373", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "UUAAUU", "nts_long": "///2/1367,///2/1368,///2/1369,///2/1370,///2/1371,///2/1372" } ] }, { "index": 28, "type": "hairpin loop", "bridging_nts": [ 5 ], "stem_indices": [ 78 ], "summary": "[1] 5 [2.1460 2.1466] 5", "num_nts": 7, "nts_short": "CGUUCAG", "nts_long": "///2/1460,///2/1461,///2/1462,///2/1463,///2/1464,///2/1465,///2/1466", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "GUUCA", "nts_long": "///2/1461,///2/1462,///2/1463,///2/1464,///2/1465" } ] }, { "index": 29, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 80 ], "summary": "[1] 4 [2.1565 2.1570] 4", "num_nts": 6, "nts_short": "CGGCAG", "nts_long": "///2/1565,///2/1566,///2/1567,///2/1568,///2/1569,///2/1570", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GGCA", "nts_long": "///2/1566,///2/1567,///2/1568,///2/1569" } ] }, { "index": 30, "type": "hairpin loop", "bridging_nts": [ 12 ], "stem_indices": [ 81 ], "summary": "[1] 12 [2.1613 2.1626] 4", "num_nts": 14, "nts_short": "GAUUGCAAUUAUUC", "nts_long": "///2/1613,///2/1614,///2/1615,///2/1616,///2/1617,///2/1618,///2/1619,///2/1620,///2/1621,///2/1622,///2/1623,///2/1624,///2/1625,///2/1626", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 12, "nts_short": "AUUGCAAUUAUU", "nts_long": "///2/1614,///2/1615,///2/1616,///2/1617,///2/1618,///2/1619,///2/1620,///2/1621,///2/1622,///2/1623,///2/1624,///2/1625" } ] }, { "index": 31, "type": "hairpin loop", "bridging_nts": [ 7 ], "stem_indices": [ 83 ], "summary": "[1] 7 [2.1658 2.1666] 2", "num_nts": 9, "nts_short": "GUCAUAAGC", "nts_long": "///2/1658,///2/1659,///2/1660,///2/1661,///2/1662,///2/1663,///2/1664,///2/1665,///2/1666", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 7, "nts_short": "UCAUAAG", "nts_long": "///2/1659,///2/1660,///2/1661,///2/1662,///2/1663,///2/1664,///2/1665" } ] }, { "index": 32, "type": "hairpin loop", "bridging_nts": [ 4 ], "stem_indices": [ 90 ], "summary": "[1] 4 [2.1847 2.1852] 9", "num_nts": 6, "nts_short": "GUGAAC", "nts_long": "///2/1847,///2/1848,///2/1849,///2/1850,///2/1851,///2/1852", "num_stems": 1, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "UGAA", "nts_long": "///2/1848,///2/1849,///2/1850,///2/1851" } ] } ], "num_bulges": 17, "bulges": [ { "index": 1, "type": "bulge", "bridging_nts": [ 1, 0 ], "stem_indices": [ 6, 7 ], "summary": "[2] 1 0 [2.49 2.477 2.51 2.476] 3 3", "num_nts": 5, "nts_short": "CAUAG", "nts_long": "///2/49,///2/50,///2/51,///2/476,///2/477", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///2/50" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 2, "type": "bulge", "bridging_nts": [ 1, 0 ], "stem_indices": [ -12, 21 ], "summary": "[2] 1 0 [2.312 2.337 2.314 2.336] 1 4", "num_nts": 5, "nts_short": "GAUAC", "nts_long": "///2/312,///2/313,///2/314,///2/336,///2/337", "num_stems": 2, "bridges": [ { "index": 1, 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"bulge", "bridging_nts": [ 1, 0 ], "stem_indices": [ 67, 68 ], "summary": "[2] 1 0 [2.1206 2.1692 2.1208 2.1691] 3 3", "num_nts": 5, "nts_short": "GGAUU", "nts_long": "///2/1206,///2/1207,///2/1208,///2/1691,///2/1692", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///2/1207" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 11, "type": "bulge", "bridging_nts": [ 1, 0 ], "stem_indices": [ -39, 76 ], "summary": "[2] 1 0 [2.1363 2.1375 2.1365 2.1374] 1 2", "num_nts": 5, "nts_short": "CUGCG", "nts_long": "///2/1363,///2/1364,///2/1365,///2/1374,///2/1375", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///2/1364" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 12, "type": "bulge", "bridging_nts": [ 0, 1 ], "stem_indices": [ -40, -41 ], "summary": "[2] 0 1 [2.1390 2.1481 2.1391 2.1479] 1 1", "num_nts": 5, "nts_short": "UCGAG", "nts_long": "///2/1390,///2/1391,///2/1479,///2/1480,///2/1481", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///2/1480" } ] }, { "index": 13, "type": "bulge", "bridging_nts": [ 2, 0 ], "stem_indices": [ -7, 13 ], "summary": "[2] 2 0 [2.112 2.349 2.115 2.348] 1 2", "num_nts": 6, "nts_short": "UGGUAA", "nts_long": "///2/112,///2/113,///2/114,///2/115,///2/348,///2/349", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "GG", "nts_long": "///2/113,///2/114" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 14, "type": "bulge", "bridging_nts": [ 0, 2 ], "stem_indices": [ 43, 44 ], "summary": "[2] 0 2 [2.802 2.863 2.803 2.860] 2 3", "num_nts": 6, "nts_short": "ACGAAU", "nts_long": "///2/802,///2/803,///2/860,///2/861,///2/862,///2/863", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 2, "nts_short": "AA", "nts_long": "///2/861,///2/862" } ] }, { "index": 15, "type": "bulge", "bridging_nts": [ 0, 2 ], "stem_indices": [ -28, 50 ], "summary": "[2] 0 2 [2.922 2.1022 2.923 2.1019] 1 2", "num_nts": 6, "nts_short": "AGCAUU", "nts_long": "///2/922,///2/923,///2/1019,///2/1020,///2/1021,///2/1022", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 2, "nts_short": "AU", "nts_long": "///2/1020,///2/1021" } ] }, { "index": 16, "type": "bulge", "bridging_nts": [ 3, 0 ], "stem_indices": [ 30, -15 ], "summary": "[2] 3 0 [2.491 2.509 2.495 2.508] 3 1", "num_nts": 7, "nts_short": "CCACUAG", "nts_long": "///2/491,///2/492,///2/493,///2/494,///2/495,///2/508,///2/509", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "CAC", "nts_long": "///2/492,///2/493,///2/494" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 17, "type": "bulge", "bridging_nts": [ 4, 0 ], "stem_indices": [ 23, 24 ], "summary": "[2] 4 0 [2.366 2.394 2.371 2.393] 3 7", "num_nts": 8, "nts_short": "UUUCGAUG", "nts_long": "///2/366,///2/367,///2/368,///2/369,///2/370,///2/371,///2/393,///2/394", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "UUCG", "nts_long": "///2/367,///2/368,///2/369,///2/370" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" } ] } ], "num_iloops": 62, "iloops": [ { "index": 1, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ -1, 2 ], "summary": "[2] 1 1 [2.10 2.1201 2.12 2.1199] 1 3", "num_nts": 6, "nts_short": "GAUAAU", "nts_long": "///2/10,///2/11,///2/12,///2/1199,///2/1200,///2/1201", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///2/11" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///2/1200" } ] }, { "index": 2, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 3, 4 ], "summary": "[2] 1 1 [2.23 2.651 2.25 2.649] 3 6", "num_nts": 6, "nts_short": "GCAUAU", "nts_long": "///2/23,///2/24,///2/25,///2/649,///2/650,///2/651", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "C", "nts_long": "///2/24" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///2/650" } ] }, { "index": 3, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ -2, 5 ], "summary": "[2] 1 1 [2.34 2.521 2.36 2.519] 1 2", "num_nts": 6, "nts_short": "UCUAAA", "nts_long": "///2/34,///2/35,///2/36,///2/519,///2/520,///2/521", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "C", "nts_long": "///2/35" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///2/520" } ] }, { "index": 4, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 12, -6 ], "summary": "[2] 1 1 [2.108 2.353 2.110 2.351] 3 1", "num_nts": 6, "nts_short": "GUUGUC", "nts_long": "///2/108,///2/109,///2/110,///2/351,///2/352,///2/353", 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"num_nts": 1, "nts_short": "G", "nts_long": "///2/165" } ] }, { "index": 7, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 27, 28 ], "summary": "[2] 1 1 [2.437 2.456 2.439 2.454] 2 3", "num_nts": 6, "nts_short": "GGAUAC", "nts_long": "///2/437,///2/438,///2/439,///2/454,///2/455,///2/456", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///2/438" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///2/455" } ] }, { "index": 8, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ -13, 29 ], "summary": "[2] 1 1 [2.459 2.470 2.461 2.468] 1 2", "num_nts": 6, "nts_short": "CAUAAG", "nts_long": "///2/459,///2/460,///2/461,///2/468,///2/469,///2/470", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///2/460" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///2/469" } ] }, { "index": 9, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ -21, -22 ], "summary": "[2] 1 1 [2.663 2.1164 2.665 2.1162] 1 1", "num_nts": 6, "nts_short": "CAGCCG", "nts_long": "///2/663,///2/664,///2/665,///2/1162,///2/1163,///2/1164", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///2/664" }, { "index": 2, "num_nts": 1, "nts_short": "C", "nts_long": "///2/1163" } ] }, { "index": 10, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ -24, 41 ], "summary": "[2] 1 1 [2.673 2.1032 2.675 2.1030] 1 2", "num_nts": 6, "nts_short": "GCUAAC", "nts_long": "///2/673,///2/674,///2/675,///2/1030,///2/1031,///2/1032", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "C", "nts_long": "///2/674" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///2/1031" } ] }, { "index": 11, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 44, -25 ], "summary": "[2] 1 1 [2.805 2.858 2.807 2.856] 3 1", "num_nts": 6, "nts_short": "UUGCUA", "nts_long": "///2/805,///2/806,///2/807,///2/856,///2/857,///2/858", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///2/806" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///2/857" } ] }, { "index": 12, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ -26, 48 ], "summary": "[2] 1 1 [2.874 2.912 2.876 2.910] 1 2", "num_nts": 6, "nts_short": "GACGCC", "nts_long": "///2/874,///2/875,///2/876,///2/910,///2/911,///2/912", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///2/875" }, { "index": 2, "num_nts": 1, "nts_short": "C", "nts_long": "///2/911" } ] }, { "index": 13, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 48, 49 ], "summary": "[2] 1 1 [2.877 2.909 2.879 2.907] 2 3", "num_nts": 6, "nts_short": "CGCGAG", "nts_long": "///2/877,///2/878,///2/879,///2/907,///2/908,///2/909", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///2/878" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///2/908" } ] }, { "index": 14, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 52, 53 ], "summary": "[2] 1 1 [2.943 2.983 2.945 2.981] 3 8", "num_nts": 6, "nts_short": "UAUAGA", "nts_long": "///2/943,///2/944,///2/945,///2/981,///2/982,///2/983", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///2/944" }, { "index": 2, "num_nts": 1, "nts_short": "G", "nts_long": "///2/982" } ] }, { "index": 15, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ -33, 61 ], "summary": "[2] 1 1 [2.1101 2.1131 2.1103 2.1129] 1 6", "num_nts": 6, "nts_short": "UGCGGG", "nts_long": "///2/1101,///2/1102,///2/1103,///2/1129,///2/1130,///2/1131", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///2/1102" }, { "index": 2, "num_nts": 1, "nts_short": "G", "nts_long": "///2/1130" } ] }, { "index": 16, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 68, 69 ], "summary": "[2] 1 1 [2.1210 2.1689 2.1212 2.1687] 3 3", "num_nts": 6, "nts_short": "GGGCCC", "nts_long": "///2/1210,///2/1211,///2/1212,///2/1687,///2/1688,///2/1689", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///2/1211" }, { "index": 2, "num_nts": 1, "nts_short": "C", "nts_long": "///2/1688" } ] }, { "index": 17, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ -37, 72 ], "summary": "[2] 1 1 [2.1277 2.1320 2.1279 2.1318] 1 3", "num_nts": 6, "nts_short": "CACGUG", "nts_long": "///2/1277,///2/1278,///2/1279,///2/1318,///2/1319,///2/1320", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///2/1278" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///2/1319" } ] }, { "index": 18, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 73, 74 ], "summary": "[2] 1 1 [2.1347 2.1382 2.1349 2.1380] 3 2", "num_nts": 6, "nts_short": "UGGCGA", "nts_long": "///2/1347,///2/1348,///2/1349,///2/1380,///2/1381,///2/1382", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///2/1348" }, { "index": 2, "num_nts": 1, "nts_short": "G", "nts_long": "///2/1381" } ] }, { "index": 19, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 82, 83 ], "summary": "[2] 1 1 [2.1655 2.1669 2.1657 2.1667] 5 2", "num_nts": 6, "nts_short": "CGGUUG", "nts_long": "///2/1655,///2/1656,///2/1657,///2/1667,///2/1668,///2/1669", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///2/1656" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///2/1668" } ] }, { "index": 20, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 84, -52 ], "summary": "[2] 1 1 [2.1706 2.1828 2.1708 2.1826] 2 1", "num_nts": 6, "nts_short": "GUCGUC", "nts_long": "///2/1706,///2/1707,///2/1708,///2/1826,///2/1827,///2/1828", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "U", "nts_long": "///2/1707" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///2/1827" } ] }, { "index": 21, "type": "symmetric internal loop", "bridging_nts": [ 1, 1 ], "stem_indices": [ 85, 86 ], "summary": "[2] 1 1 [2.1714 2.1819 2.1716 2.1817] 3 2", "num_nts": 6, "nts_short": "UACGAA", "nts_long": "///2/1714,///2/1715,///2/1716,///2/1817,///2/1818,///2/1819", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///2/1715" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///2/1818" } ] }, { "index": 22, "type": "asymmetric internal loop", "bridging_nts": [ 1, 2 ], "stem_indices": [ -50, -51 ], "summary": "[2] 1 2 [2.1700 2.1836 2.1702 2.1833] 1 1", "num_nts": 7, "nts_short": "CCGCAAG", "nts_long": "///2/1700,///2/1701,///2/1702,///2/1833,///2/1834,///2/1835,///2/1836", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "C", "nts_long": "///2/1701" }, { "index": 2, "num_nts": 2, "nts_short": "AA", "nts_long": "///2/1834,///2/1835" } ] }, { "index": 23, "type": "symmetric internal loop", "bridging_nts": [ 2, 2 ], "stem_indices": [ 33, 34 ], "summary": "[2] 2 2 [2.535 2.548 2.538 2.545] 2 2", "num_nts": 8, "nts_short": "GACUAGGC", "nts_long": "///2/535,///2/536,///2/537,///2/538,///2/545,///2/546,///2/547,///2/548", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "AC", "nts_long": "///2/536,///2/537" }, { "index": 2, "num_nts": 2, "nts_short": "GG", "nts_long": "///2/546,///2/547" } ] }, { "index": 24, "type": "symmetric internal loop", "bridging_nts": [ 2, 2 ], "stem_indices": [ 35, -18 ], "summary": "[2] 2 2 [2.566 2.584 2.569 2.581] 2 1", "num_nts": 8, "nts_short": "UCCAUUAA", "nts_long": "///2/566,///2/567,///2/568,///2/569,///2/581,///2/582,///2/583,///2/584", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "CC", "nts_long": "///2/567,///2/568" }, { "index": 2, "num_nts": 2, "nts_short": "UA", "nts_long": "///2/582,///2/583" } ] }, { "index": 25, "type": "symmetric internal loop", "bridging_nts": [ 2, 2 ], "stem_indices": [ 60, -33 ], "summary": "[2] 2 2 [2.1098 2.1134 2.1101 2.1131] 3 1", "num_nts": 8, "nts_short": "CGAUGCAG", "nts_long": "///2/1098,///2/1099,///2/1100,///2/1101,///2/1131,///2/1132,///2/1133,///2/1134", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "GA", "nts_long": "///2/1099,///2/1100" }, { "index": 2, "num_nts": 2, "nts_short": "CA", "nts_long": "///2/1132,///2/1133" } ] }, { "index": 26, "type": "symmetric internal loop", "bridging_nts": [ 2, 2 ], "stem_indices": [ -43, -44 ], "summary": "[2] 2 2 [2.1399 2.1447 2.1402 2.1444] 1 1", "num_nts": 8, "nts_short": "CUAAUUAG", "nts_long": "///2/1399,///2/1400,///2/1401,///2/1402,///2/1444,///2/1445,///2/1446,///2/1447", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "UA", "nts_long": "///2/1400,///2/1401" }, { "index": 2, "num_nts": 2, "nts_short": "UA", "nts_long": "///2/1445,///2/1446" } ] }, { "index": 27, "type": "symmetric internal loop", "bridging_nts": [ 2, 2 ], "stem_indices": [ -44, 77 ], "summary": "[2] 2 2 [2.1402 2.1444 2.1405 2.1441] 1 2", "num_nts": 8, "nts_short": "ACUAUUCU", "nts_long": "///2/1402,///2/1403,///2/1404,///2/1405,///2/1441,///2/1442,///2/1443,///2/1444", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "CU", "nts_long": "///2/1403,///2/1404" }, { "index": 2, "num_nts": 2, "nts_short": "UC", "nts_long": "///2/1442,///2/1443" } ] }, { "index": 28, "type": "symmetric internal loop", "bridging_nts": [ 2, 2 ], "stem_indices": [ 79, 80 ], "summary": "[2] 2 2 [2.1559 2.1576 2.1562 2.1573] 2 4", "num_nts": 8, "nts_short": "CUACGCGG", "nts_long": "///2/1559,///2/1560,///2/1561,///2/1562,///2/1573,///2/1574,///2/1575,///2/1576", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "UA", "nts_long": "///2/1560,///2/1561" }, { "index": 2, "num_nts": 2, "nts_short": "CG", "nts_long": "///2/1574,///2/1575" } ] }, { "index": 29, "type": "symmetric internal loop", "bridging_nts": [ 2, 2 ], "stem_indices": [ 86, -53 ], "summary": "[2] 2 2 [2.1717 2.1816 2.1720 2.1813] 2 1", "num_nts": 8, "nts_short": "CGAUAGAG", "nts_long": "///2/1717,///2/1718,///2/1719,///2/1720,///2/1813,///2/1814,///2/1815,///2/1816", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "GA", "nts_long": "///2/1718,///2/1719" }, { "index": 2, "num_nts": 2, "nts_short": "GA", "nts_long": "///2/1814,///2/1815" } ] }, { "index": 30, "type": "symmetric internal loop", "bridging_nts": [ 2, 2 ], "stem_indices": [ 87, 88 ], "summary": "[2] 2 2 [2.1738 2.1796 2.1741 2.1793] 3 2", "num_nts": 8, "nts_short": "CCCUACGG", "nts_long": "///2/1738,///2/1739,///2/1740,///2/1741,///2/1793,///2/1794,///2/1795,///2/1796", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "CC", "nts_long": "///2/1739,///2/1740" }, { "index": 2, "num_nts": 2, "nts_short": "CG", "nts_long": "///2/1794,///2/1795" } ] }, { "index": 31, "type": "asymmetric internal loop", "bridging_nts": [ 2, 3 ], "stem_indices": [ 5, -3 ], "summary": "[2] 2 3 [2.37 2.518 2.40 2.514] 2 1", "num_nts": 9, "nts_short": "CAAAUGACG", "nts_long": "///2/37,///2/38,///2/39,///2/40,///2/514,///2/515,///2/516,///2/517,///2/518", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "AA", "nts_long": "///2/38,///2/39" }, { "index": 2, "num_nts": 3, "nts_short": "GAC", "nts_long": "///2/515,///2/516,///2/517" } ] }, { "index": 32, "type": "asymmetric internal loop", "bridging_nts": [ 4, 1 ], "stem_indices": [ 8, 9 ], "summary": "[2] 4 1 [2.57 2.88 2.62 2.86] 2 2", "num_nts": 9, "nts_short": "UCUAAGCUG", "nts_long": "///2/57,///2/58,///2/59,///2/60,///2/61,///2/62,///2/86,///2/87,///2/88", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "CUAA", "nts_long": "///2/58,///2/59,///2/60,///2/61" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///2/87" } ] }, { "index": 33, "type": "asymmetric internal loop", "bridging_nts": [ 1, 4 ], "stem_indices": [ 25, 26 ], "summary": "[2] 1 4 [2.411 2.429 2.413 2.424] 3 4", "num_nts": 9, "nts_short": "GGGCGAUUC", "nts_long": "///2/411,///2/412,///2/413,///2/424,///2/425,///2/426,///2/427,///2/428,///2/429", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///2/412" }, { "index": 2, "num_nts": 4, "nts_short": "GAUU", "nts_long": "///2/425,///2/426,///2/427,///2/428" } ] }, { "index": 34, "type": "asymmetric internal loop", "bridging_nts": [ 2, 3 ], "stem_indices": [ 50, -29 ], "summary": "[2] 2 3 [2.924 2.1018 2.927 2.1014] 2 1", "num_nts": 9, "nts_short": "GGACGUUUU", "nts_long": "///2/924,///2/925,///2/926,///2/927,///2/1014,///2/1015,///2/1016,///2/1017,///2/1018", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "GA", "nts_long": "///2/925,///2/926" }, { "index": 2, "num_nts": 3, "nts_short": "UUU", "nts_long": "///2/1015,///2/1016,///2/1017" } ] }, { "index": 35, "type": "asymmetric internal loop", "bridging_nts": [ 3, 2 ], "stem_indices": [ -30, 51 ], "summary": "[2] 3 2 [2.931 2.1010 2.935 2.1007] 1 4", "num_nts": 9, "nts_short": "CGGGGCAAG", "nts_long": "///2/931,///2/932,///2/933,///2/934,///2/935,///2/1007,///2/1008,///2/1009,///2/1010", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "GGG", "nts_long": "///2/932,///2/933,///2/934" }, { "index": 2, "num_nts": 2, "nts_short": "AA", "nts_long": "///2/1008,///2/1009" } ] }, { "index": 36, "type": "asymmetric internal loop", "bridging_nts": [ 4, 1 ], "stem_indices": [ 56, -31 ], "summary": "[2] 4 1 [2.1042 2.1073 2.1047 2.1071] 6 1", "num_nts": 9, "nts_short": "AGGUUCGUU", "nts_long": "///2/1042,///2/1043,///2/1044,///2/1045,///2/1046,///2/1047,///2/1071,///2/1072,///2/1073", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "GGUU", "nts_long": "///2/1043,///2/1044,///2/1045,///2/1046" }, { "index": 2, "num_nts": 1, "nts_short": "U", "nts_long": "///2/1072" } ] }, { "index": 37, "type": "asymmetric internal loop", "bridging_nts": [ 2, 3 ], "stem_indices": [ 69, 70 ], "summary": "[2] 2 3 [2.1214 2.1685 2.1217 2.1681] 3 2", "num_nts": 9, "nts_short": "ACCAUCCCU", "nts_long": "///2/1214,///2/1215,///2/1216,///2/1217,///2/1681,///2/1682,///2/1683,///2/1684,///2/1685", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "CC", "nts_long": "///2/1215,///2/1216" }, { "index": 2, "num_nts": 3, "nts_short": "CCC", "nts_long": "///2/1682,///2/1683,///2/1684" } ] }, { "index": 38, "type": "asymmetric internal loop", "bridging_nts": [ 3, 2 ], "stem_indices": [ -42, -43 ], "summary": "[2] 3 2 [2.1395 2.1450 2.1399 2.1447] 1 1", "num_nts": 9, "nts_short": "CAUGCGAGG", "nts_long": "///2/1395,///2/1396,///2/1397,///2/1398,///2/1399,///2/1447,///2/1448,///2/1449,///2/1450", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "AUG", "nts_long": "///2/1396,///2/1397,///2/1398" }, { "index": 2, "num_nts": 2, "nts_short": "AG", "nts_long": "///2/1448,///2/1449" } ] }, { "index": 39, "type": "asymmetric internal loop", "bridging_nts": [ 2, 3 ], "stem_indices": [ -51, 84 ], "summary": "[2] 2 3 [2.1702 2.1833 2.1705 2.1829] 1 2", "num_nts": 9, "nts_short": "GCCCGUAAC", "nts_long": "///2/1702,///2/1703,///2/1704,///2/1705,///2/1829,///2/1830,///2/1831,///2/1832,///2/1833", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "CC", "nts_long": "///2/1703,///2/1704" }, { "index": 2, "num_nts": 3, "nts_short": "UAA", "nts_long": "///2/1830,///2/1831,///2/1832" } ] }, { "index": 40, "type": "asymmetric internal loop", "bridging_nts": [ 5, 1 ], "stem_indices": [ -4, 6 ], "summary": "[2] 5 1 [2.41 2.481 2.47 2.479] 1 3", "num_nts": 10, "nts_short": "GAUUAAGCGC", "nts_long": "///2/41,///2/42,///2/43,///2/44,///2/45,///2/46,///2/47,///2/479,///2/480,///2/481", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "AUUAA", "nts_long": "///2/42,///2/43,///2/44,///2/45,///2/46" }, { "index": 2, "num_nts": 1, "nts_short": "G", "nts_long": "///2/480" } ] }, { "index": 41, "type": "symmetric internal loop", "bridging_nts": [ 3, 3 ], "stem_indices": [ 18, 19 ], "summary": "[2] 3 3 [2.188 2.211 2.192 2.207] 4 5", "num_nts": 10, "nts_short": "CUGACGGAUG", "nts_long": "///2/188,///2/189,///2/190,///2/191,///2/192,///2/207,///2/208,///2/209,///2/210,///2/211", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "UGA", "nts_long": "///2/189,///2/190,///2/191" }, { "index": 2, "num_nts": 3, "nts_short": "GAU", "nts_long": "///2/208,///2/209,///2/210" } ] }, { "index": 42, "type": "symmetric internal loop", "bridging_nts": [ 3, 3 ], "stem_indices": [ 41, 42 ], "summary": "[2] 3 3 [2.676 2.1029 2.680 2.1025] 2 3", "num_nts": 10, "nts_short": "CGUAGUCAAG", "nts_long": "///2/676,///2/677,///2/678,///2/679,///2/680,///2/1025,///2/1026,///2/1027,///2/1028,///2/1029", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "GUA", "nts_long": "///2/677,///2/678,///2/679" }, { "index": 2, "num_nts": 3, "nts_short": "CAA", "nts_long": "///2/1026,///2/1027,///2/1028" } ] }, { "index": 43, "type": "symmetric internal loop", "bridging_nts": [ 3, 3 ], "stem_indices": [ -29, -30 ], "summary": "[2] 3 3 [2.927 2.1014 2.931 2.1010] 1 1", "num_nts": 10, "nts_short": "CGGCCGAAUG", "nts_long": "///2/927,///2/928,///2/929,///2/930,///2/931,///2/1010,///2/1011,///2/1012,///2/1013,///2/1014", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "GGC", "nts_long": "///2/928,///2/929,///2/930" }, { "index": 2, "num_nts": 3, "nts_short": "AAU", "nts_long": "///2/1011,///2/1012,///2/1013" } ] }, { "index": 44, "type": "symmetric internal loop", "bridging_nts": [ 3, 3 ], "stem_indices": [ -31, 57 ], "summary": "[2] 3 3 [2.1047 2.1071 2.1051 2.1067] 1 4", "num_nts": 10, "nts_short": "CGAAGCGUAG", "nts_long": "///2/1047,///2/1048,///2/1049,///2/1050,///2/1051,///2/1067,///2/1068,///2/1069,///2/1070,///2/1071", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "GAA", "nts_long": "///2/1048,///2/1049,///2/1050" }, { "index": 2, "num_nts": 3, "nts_short": "GUA", "nts_long": "///2/1068,///2/1069,///2/1070" } ] }, { "index": 45, "type": "asymmetric internal loop", "bridging_nts": [ 1, 5 ], "stem_indices": [ 58, 59 ], "summary": "[2] 1 5 [2.1091 2.1158 2.1093 2.1152] 3 2", "num_nts": 10, "nts_short": "CGAUCUUUGG", "nts_long": "///2/1091,///2/1092,///2/1093,///2/1152,///2/1153,///2/1154,///2/1155,///2/1156,///2/1157,///2/1158", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "G", "nts_long": "///2/1092" }, { "index": 2, "num_nts": 5, "nts_short": "CUUUG", "nts_long": "///2/1153,///2/1154,///2/1155,///2/1156,///2/1157" } ] }, { "index": 46, "type": "symmetric internal loop", "bridging_nts": [ 3, 3 ], "stem_indices": [ 88, 89 ], "summary": "[2] 3 3 [2.1742 2.1792 2.1746 2.1788] 2 5", "num_nts": 10, "nts_short": "CGGAUAGAAG", "nts_long": "///2/1742,///2/1743,///2/1744,///2/1745,///2/1746,///2/1788,///2/1789,///2/1790,///2/1791,///2/1792", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "GGA", "nts_long": "///2/1743,///2/1744,///2/1745" }, { "index": 2, "num_nts": 3, "nts_short": "GAA", "nts_long": "///2/1789,///2/1790,///2/1791" } ] }, { "index": 47, "type": "asymmetric internal loop", "bridging_nts": [ 4, 3 ], "stem_indices": [ 9, 10 ], "summary": "[2] 4 3 [2.63 2.85 2.68 2.81] 2 2", "num_nts": 11, "nts_short": "UACGCAUGAAA", "nts_long": "///2/63,///2/64,///2/65,///2/66,///2/67,///2/68,///2/81,///2/82,///2/83,///2/84,///2/85", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "ACGC", "nts_long": "///2/64,///2/65,///2/66,///2/67" }, { "index": 2, "num_nts": 3, "nts_short": "GAA", "nts_long": "///2/82,///2/83,///2/84" } ] }, { "index": 48, "type": "asymmetric internal loop", "bridging_nts": [ 4, 3 ], "stem_indices": [ 13, 14 ], "summary": "[2] 4 3 [2.116 2.347 2.121 2.343] 2 2", "num_nts": 11, "nts_short": "UCCUUUAUUCG", "nts_long": "///2/116,///2/117,///2/118,///2/119,///2/120,///2/121,///2/343,///2/344,///2/345,///2/346,///2/347", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "CCUU", "nts_long": "///2/117,///2/118,///2/119,///2/120" }, { "index": 2, "num_nts": 3, "nts_short": "UUC", "nts_long": "///2/344,///2/345,///2/346" } ] }, { "index": 49, "type": "asymmetric internal loop", "bridging_nts": [ 3, 4 ], "stem_indices": [ -16, 33 ], "summary": "[2] 3 4 [2.530 2.554 2.534 2.549] 1 2", "num_nts": 11, "nts_short": "UACAGCCUGUA", "nts_long": "///2/530,///2/531,///2/532,///2/533,///2/534,///2/549,///2/550,///2/551,///2/552,///2/553,///2/554", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "ACA", "nts_long": "///2/531,///2/532,///2/533" }, { "index": 2, "num_nts": 4, "nts_short": "CUGU", "nts_long": "///2/550,///2/551,///2/552,///2/553" } ] }, { "index": 50, "type": "asymmetric internal loop", "bridging_nts": [ 1, 6 ], "stem_indices": [ -17, 35 ], "summary": "[2] 1 6 [2.563 2.592 2.565 2.585] 1 2", "num_nts": 11, "nts_short": "GAGCGAGGAUC", "nts_long": "///2/563,///2/564,///2/565,///2/585,///2/586,///2/587,///2/588,///2/589,///2/590,///2/591,///2/592", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "A", "nts_long": "///2/564" }, { "index": 2, "num_nts": 6, "nts_short": "GAGGAU", "nts_long": "///2/586,///2/587,///2/588,///2/589,///2/590,///2/591" } ] }, { "index": 51, "type": "asymmetric internal loop", "bridging_nts": [ 3, 4 ], "stem_indices": [ -52, 85 ], "summary": "[2] 3 4 [2.1708 2.1826 2.1712 2.1821] 1 3", "num_nts": 11, "nts_short": "CGCUAUAAAAG", "nts_long": "///2/1708,///2/1709,///2/1710,///2/1711,///2/1712,///2/1821,///2/1822,///2/1823,///2/1824,///2/1825,///2/1826", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "GCU", "nts_long": "///2/1709,///2/1710,///2/1711" }, { "index": 2, "num_nts": 4, "nts_short": "AAAA", "nts_long": "///2/1822,///2/1823,///2/1824,///2/1825" } ] }, { "index": 52, "type": "asymmetric internal loop", "bridging_nts": [ 3, 6 ], "stem_indices": [ 53, 54 ], "summary": "[2] 3 6 [2.952 2.974 2.956 2.967] 8 2 k-turn:normal", "num_nts": 13, "nts_short": "GCUAGCUUGGACC", "nts_long": "///2/952,///2/953,///2/954,///2/955,///2/956,///2/967,///2/968,///2/969,///2/970,///2/971,///2/972,///2/973,///2/974", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "CUA", "nts_long": "///2/953,///2/954,///2/955" }, { "index": 2, "num_nts": 6, "nts_short": "UUGGAC", "nts_long": "///2/968,///2/969,///2/970,///2/971,///2/972,///2/973" } ] }, { "index": 53, "type": "asymmetric internal loop", "bridging_nts": [ 3, 7 ], "stem_indices": [ -10, 20 ], "summary": "[2] 3 7 [2.216 2.309 2.220 2.301] 1 4", "num_nts": 14, "nts_short": "CAUUUAACCUCGGG", "nts_long": "///2/216,///2/217,///2/218,///2/219,///2/220,///2/301,///2/302,///2/303,///2/304,///2/305,///2/306,///2/307,///2/308,///2/309", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "AUU", "nts_long": "///2/217,///2/218,///2/219" }, { "index": 2, "num_nts": 7, "nts_short": "ACCUCGG", "nts_long": "///2/302,///2/303,///2/304,///2/305,///2/306,///2/307,///2/308" } ] }, { "index": 54, "type": "asymmetric internal loop", "bridging_nts": [ 4, 6 ], "stem_indices": [ 22, 23 ], "summary": "[2] 4 6 [2.359 2.403 2.364 2.396] 3 3", "num_nts": 14, "nts_short": "UAUCAAUGACCACG", "nts_long": "///2/359,///2/360,///2/361,///2/362,///2/363,///2/364,///2/396,///2/397,///2/398,///2/399,///2/400,///2/401,///2/402,///2/403", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 4, "nts_short": "AUCA", "nts_long": "///2/360,///2/361,///2/362,///2/363" }, { "index": 2, "num_nts": 6, "nts_short": "GACCAC", "nts_long": "///2/397,///2/398,///2/399,///2/400,///2/401,///2/402" } ] }, { "index": 55, "type": "asymmetric internal loop", "bridging_nts": [ 6, 4 ], "stem_indices": [ 64, 65 ], "summary": "[2] 6 4 [2.1168 2.1191 2.1175 2.1186] 3 4", "num_nts": 14, "nts_short": "GGAGUAUGUGAAAC", "nts_long": "///2/1168,///2/1169,///2/1170,///2/1171,///2/1172,///2/1173,///2/1174,///2/1175,///2/1186,///2/1187,///2/1188,///2/1189,///2/1190,///2/1191", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 6, "nts_short": "GAGUAU", "nts_long": "///2/1169,///2/1170,///2/1171,///2/1172,///2/1173,///2/1174" }, { "index": 2, "num_nts": 4, "nts_short": "GAAA", "nts_long": "///2/1187,///2/1188,///2/1189,///2/1190" } ] }, { "index": 56, "type": "symmetric internal loop", "bridging_nts": [ 5, 5 ], "stem_indices": [ -49, 81 ], "summary": "[2] 5 5 [2.1604 2.1635 2.1610 2.1629] 1 4", "num_nts": 14, "nts_short": "GGGAUCGCAUGAAC", "nts_long": "///2/1604,///2/1605,///2/1606,///2/1607,///2/1608,///2/1609,///2/1610,///2/1629,///2/1630,///2/1631,///2/1632,///2/1633,///2/1634,///2/1635", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "GGAUC", "nts_long": "///2/1605,///2/1606,///2/1607,///2/1608,///2/1609" }, { "index": 2, "num_nts": 5, "nts_short": "AUGAA", "nts_long": "///2/1630,///2/1631,///2/1632,///2/1633,///2/1634" } ] }, { "index": 57, "type": "asymmetric internal loop", "bridging_nts": [ 5, 6 ], "stem_indices": [ 15, 16 ], "summary": "[2] 5 6 [2.145 2.174 2.151 2.167] 2 2", "num_nts": 15, "nts_short": "GGAUAACGCUAAUAC", "nts_long": "///2/145,///2/146,///2/147,///2/148,///2/149,///2/150,///2/151,///2/167,///2/168,///2/169,///2/170,///2/171,///2/172,///2/173,///2/174", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "GAUAA", "nts_long": "///2/146,///2/147,///2/148,///2/149,///2/150" }, { "index": 2, "num_nts": 6, "nts_short": "CUAAUA", "nts_long": "///2/168,///2/169,///2/170,///2/171,///2/172,///2/173" } ] }, { "index": 58, "type": "asymmetric internal loop", "bridging_nts": [ 7, 4 ], "stem_indices": [ -48, 79 ], "summary": "[2] 7 4 [2.1550 2.1582 2.1558 2.1577] 1 2", "num_nts": 15, "nts_short": "GUGCCUACCGUAACC", "nts_long": "///2/1550,///2/1551,///2/1552,///2/1553,///2/1554,///2/1555,///2/1556,///2/1557,///2/1558,///2/1577,///2/1578,///2/1579,///2/1580,///2/1581,///2/1582", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 7, "nts_short": "UGCCUAC", "nts_long": "///2/1551,///2/1552,///2/1553,///2/1554,///2/1555,///2/1556,///2/1557" }, { "index": 2, "num_nts": 4, "nts_short": "UAAC", "nts_long": "///2/1578,///2/1579,///2/1580,///2/1581" } ] }, { "index": 59, "type": "asymmetric internal loop", "bridging_nts": [ 5, 7 ], "stem_indices": [ 38, 39 ], "summary": "[2] 5 7 [2.611 2.632 2.617 2.624] 4 2", "num_nts": 16, "nts_short": "GUGCCAGCGGUAAUUC", "nts_long": "///2/611,///2/612,///2/613,///2/614,///2/615,///2/616,///2/617,///2/624,///2/625,///2/626,///2/627,///2/628,///2/629,///2/630,///2/631,///2/632", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "UGCCA", "nts_long": "///2/612,///2/613,///2/614,///2/615,///2/616" }, { "index": 2, "num_nts": 7, "nts_short": "GGUAAUU", "nts_long": "///2/625,///2/626,///2/627,///2/628,///2/629,///2/630,///2/631" } ] }, { "index": 60, "type": "asymmetric internal loop", "bridging_nts": [ 7, 6 ], "stem_indices": [ -25, 45 ], "summary": "[2] 7 6 [2.807 2.856 2.815 2.849] 1 2", "num_nts": 17, "nts_short": "GAAAAAAUUACCGCAGC", "nts_long": "///2/807,///2/808,///2/809,///2/810,///2/811,///2/812,///2/813,///2/814,///2/815,///2/849,///2/850,///2/851,///2/852,///2/853,///2/854,///2/855,///2/856", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 7, "nts_short": "AAAAAAU", "nts_long": "///2/808,///2/809,///2/810,///2/811,///2/812,///2/813,///2/814" }, { "index": 2, "num_nts": 6, "nts_short": "CCGCAG", "nts_long": "///2/850,///2/851,///2/852,///2/853,///2/854,///2/855" } ] }, { "index": 61, "type": "asymmetric internal loop", "bridging_nts": [ 13, 14 ], "stem_indices": [ -47, -48 ], "summary": "[2] 13 14 [2.1536 2.1597 2.1550 2.1582] 1 1", "num_nts": 31, "nts_short": "GACUGGCUCAGCGUGCCGUUGAACCCCAUUC", "nts_long": "///2/1536,///2/1537,///2/1538,///2/1539,///2/1540,///2/1541,///2/1542,///2/1543,///2/1544,///2/1545,///2/1546,///2/1547,///2/1548,///2/1549,///2/1550,///2/1582,///2/1583,///2/1584,///2/1585,///2/1586,///2/1587,///2/1588,///2/1589,///2/1590,///2/1591,///2/1592,///2/1593,///2/1594,///2/1595,///2/1596,///2/1597", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 13, "nts_short": "ACUGGCUCAGCGU", "nts_long": "///2/1537,///2/1538,///2/1539,///2/1540,///2/1541,///2/1542,///2/1543,///2/1544,///2/1545,///2/1546,///2/1547,///2/1548,///2/1549" }, { "index": 2, "num_nts": 14, "nts_short": "CGUUGAACCCCAUU", "nts_long": "///2/1583,///2/1584,///2/1585,///2/1586,///2/1587,///2/1588,///2/1589,///2/1590,///2/1591,///2/1592,///2/1593,///2/1594,///2/1595,///2/1596" } ] }, { "index": 62, "type": "asymmetric internal loop", "bridging_nts": [ 15, 14 ], "stem_indices": [ -53, 87 ], "summary": "[2] 15 14 [2.1720 2.1813 2.1736 2.1798] 1 3", "num_nts": 33, "nts_short": "UUGGAUGGUUUAGUGAGCGAACUUGACUAUCUA", "nts_long": "///2/1720,///2/1721,///2/1722,///2/1723,///2/1724,///2/1725,///2/1726,///2/1727,///2/1728,///2/1729,///2/1730,///2/1731,///2/1732,///2/1733,///2/1734,///2/1735,///2/1736,///2/1798,///2/1799,///2/1800,///2/1801,///2/1802,///2/1803,///2/1804,///2/1805,///2/1806,///2/1807,///2/1808,///2/1809,///2/1810,///2/1811,///2/1812,///2/1813", "num_stems": 2, "bridges": [ { "index": 1, "num_nts": 15, "nts_short": "UGGAUGGUUUAGUGA", "nts_long": "///2/1721,///2/1722,///2/1723,///2/1724,///2/1725,///2/1726,///2/1727,///2/1728,///2/1729,///2/1730,///2/1731,///2/1732,///2/1733,///2/1734,///2/1735" }, { "index": 2, "num_nts": 14, "nts_short": "GAACUUGACUAUCU", "nts_long": "///2/1799,///2/1800,///2/1801,///2/1802,///2/1803,///2/1804,///2/1805,///2/1806,///2/1807,///2/1808,///2/1809,///2/1810,///2/1811,///2/1812" } ] } ], "num_junctions": 17, "junctions": [ { "index": 1, "type": "3-way junction", "bridging_nts": [ 0, 2, 3 ], "stem_indices": [ 74, 75, -39 ], "summary": "[3] 0 2 3 [2.1350 2.1379 2.1351 2.1360 2.1363 2.1375] 2 3 1", "num_nts": 11, "nts_short": "UGUGUCGAUAA", "nts_long": "///2/1350,///2/1351,///2/1360,///2/1361,///2/1362,///2/1363,///2/1375,///2/1376,///2/1377,///2/1378,///2/1379", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 2, "nts_short": "GU", "nts_long": "///2/1361,///2/1362" }, { "index": 3, "num_nts": 3, "nts_short": "AUA", "nts_long": "///2/1376,///2/1377,///2/1378" } ] }, { "index": 2, "type": "3-way junction", "bridging_nts": [ 0, 5, 1 ], "stem_indices": [ -3, -4, -14 ], "summary": "[3] 0 5 1 [2.40 2.514 2.41 2.481 2.487 2.512] 1 1 1", "num_nts": 12, "nts_short": "AGCGCAAAUAGU", "nts_long": "///2/40,///2/41,///2/481,///2/482,///2/483,///2/484,///2/485,///2/486,///2/487,///2/512,///2/513,///2/514", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 5, "nts_short": "GCAAA", "nts_long": "///2/482,///2/483,///2/484,///2/485,///2/486" }, { "index": 3, "num_nts": 1, "nts_short": "G", "nts_long": "///2/513" } ] }, { "index": 3, "type": "3-way junction", "bridging_nts": [ 2, 1, 4 ], "stem_indices": [ 45, 46, 47 ], "summary": "[3] 2 1 4 [2.816 2.848 2.819 2.829 2.831 2.843] 2 2 3", "num_nts": 13, "nts_short": "AGAGCAGCUGGAU", "nts_long": "///2/816,///2/817,///2/818,///2/819,///2/829,///2/830,///2/831,///2/843,///2/844,///2/845,///2/846,///2/847,///2/848", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "GA", "nts_long": "///2/817,///2/818" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///2/830" }, { "index": 3, "num_nts": 4, "nts_short": "UGGA", "nts_long": "///2/844,///2/845,///2/846,///2/847" } ] }, { "index": 4, "type": "3-way junction", "bridging_nts": [ 1, 3, 3 ], "stem_indices": [ 59, 60, 63 ], "summary": "[3] 1 3 3 [2.1094 2.1151 2.1096 2.1136 2.1140 2.1147] 2 3 2", "num_nts": 13, "nts_short": "CCGUUCCGCAAAG", "nts_long": "///2/1094,///2/1095,///2/1096,///2/1136,///2/1137,///2/1138,///2/1139,///2/1140,///2/1147,///2/1148,///2/1149,///2/1150,///2/1151", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 1, "nts_short": "C", "nts_long": "///2/1095" }, { "index": 2, "num_nts": 3, "nts_short": "UCC", "nts_long": "///2/1137,///2/1138,///2/1139" }, { "index": 3, "num_nts": 3, "nts_short": "AAA", "nts_long": "///2/1148,///2/1149,///2/1150" } ] }, { "index": 5, "type": "3-way junction", "bridging_nts": [ 5, 1, 5 ], "stem_indices": [ -34, -35, -46 ], "summary": "[3] 5 1 5 [2.1222 2.1644 2.1228 2.1530 2.1532 2.1638] 1 1 1", "num_nts": 17, "nts_short": "GAGUGGAUACGGAAUUC", "nts_long": "///2/1222,///2/1223,///2/1224,///2/1225,///2/1226,///2/1227,///2/1228,///2/1530,///2/1531,///2/1532,///2/1638,///2/1639,///2/1640,///2/1641,///2/1642,///2/1643,///2/1644", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 5, "nts_short": "AGUGG", "nts_long": "///2/1223,///2/1224,///2/1225,///2/1226,///2/1227" }, { "index": 2, "num_nts": 1, "nts_short": "A", "nts_long": "///2/1531" }, { "index": 3, "num_nts": 5, "nts_short": "GAAUU", "nts_long": "///2/1639,///2/1640,///2/1641,///2/1642,///2/1643" } ] }, { "index": 6, "type": "3-way junction", "bridging_nts": [ 3, 6, 2 ], "stem_indices": [ -46, -47, -49 ], "summary": "[3] 3 6 2 [2.1532 2.1638 2.1536 2.1597 2.1604 2.1635] 1 1 1", "num_nts": 17, "nts_short": "CACUGCGUGAUGGCGAG", "nts_long": "///2/1532,///2/1533,///2/1534,///2/1535,///2/1536,///2/1597,///2/1598,///2/1599,///2/1600,///2/1601,///2/1602,///2/1603,///2/1604,///2/1635,///2/1636,///2/1637,///2/1638", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "ACU", "nts_long": "///2/1533,///2/1534,///2/1535" }, { "index": 2, "num_nts": 6, "nts_short": "GUGAUG", "nts_long": "///2/1598,///2/1599,///2/1600,///2/1601,///2/1602,///2/1603" }, { "index": 3, "num_nts": 2, "nts_short": "GA", "nts_long": "///2/1636,///2/1637" } ] }, { "index": 7, "type": "3-way junction", "bridging_nts": [ 2, 7, 3 ], "stem_indices": [ 51, 52, 55 ], "summary": "[3] 2 7 3 [2.938 2.1004 2.941 2.985 2.993 2.1000] 4 3 2", "num_nts": 18, "nts_short": "AUUCGGACCAGAGCAUUU", "nts_long": "///2/938,///2/939,///2/940,///2/941,///2/985,///2/986,///2/987,///2/988,///2/989,///2/990,///2/991,///2/992,///2/993,///2/1000,///2/1001,///2/1002,///2/1003,///2/1004", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "UU", "nts_long": "///2/939,///2/940" }, { "index": 2, "num_nts": 7, "nts_short": "GACCAGA", "nts_long": "///2/986,///2/987,///2/988,///2/989,///2/990,///2/991,///2/992" }, { "index": 3, "num_nts": 3, "nts_short": "AUU", "nts_long": "///2/1001,///2/1002,///2/1003" } ] }, { "index": 8, "type": "3-way junction", "bridging_nts": [ 3, 6, 6 ], "stem_indices": [ 70, -34, 82 ], "summary": "[3] 3 6 6 [2.1218 2.1680 2.1222 2.1644 2.1651 2.1673] 2 1 5", "num_nts": 21, "nts_short": "CCAGGCCCAGUAAUGAUUAAG", "nts_long": "///2/1218,///2/1219,///2/1220,///2/1221,///2/1222,///2/1644,///2/1645,///2/1646,///2/1647,///2/1648,///2/1649,///2/1650,///2/1651,///2/1673,///2/1674,///2/1675,///2/1676,///2/1677,///2/1678,///2/1679,///2/1680", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "CAG", "nts_long": "///2/1219,///2/1220,///2/1221" }, { "index": 2, "num_nts": 6, "nts_short": "CCAGUA", "nts_long": "///2/1645,///2/1646,///2/1647,///2/1648,///2/1649,///2/1650" }, { "index": 3, "num_nts": 6, "nts_short": "GAUUAA", "nts_long": "///2/1674,///2/1675,///2/1676,///2/1677,///2/1678,///2/1679" } ] }, { "index": 9, "type": "3-way junction", "bridging_nts": [ 3, 5, 8 ], "stem_indices": [ -41, -42, 78 ], "summary": "[3] 3 5 8 [2.1391 2.1479 2.1395 2.1450 2.1456 2.1470] 1 1 5", "num_nts": 22, "nts_short": "CUGGCGGACAAGCCCGAGAUUG", "nts_long": "///2/1391,///2/1392,///2/1393,///2/1394,///2/1395,///2/1450,///2/1451,///2/1452,///2/1453,///2/1454,///2/1455,///2/1456,///2/1470,///2/1471,///2/1472,///2/1473,///2/1474,///2/1475,///2/1476,///2/1477,///2/1478,///2/1479", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "UGG", "nts_long": "///2/1392,///2/1393,///2/1394" }, { "index": 2, "num_nts": 5, "nts_short": "GACAA", "nts_long": "///2/1451,///2/1452,///2/1453,///2/1454,///2/1455" }, { "index": 3, "num_nts": 8, "nts_short": "CCGAGAUU", "nts_long": "///2/1471,///2/1472,///2/1473,///2/1474,///2/1475,///2/1476,///2/1477,///2/1478" } ] }, { "index": 10, "type": "3-way junction", "bridging_nts": [ 11, 5, 16 ], "stem_indices": [ -38, 73, -40 ], "summary": "[3] 11 5 16 [2.1333 2.1498 2.1345 2.1384 2.1390 2.1481] 1 3 1", "num_nts": 38, "nts_short": "UGGCCGUUCUUAGCGAGACUGCAAUAACAGGUCUGUGA", "nts_long": "///2/1333,///2/1334,///2/1335,///2/1336,///2/1337,///2/1338,///2/1339,///2/1340,///2/1341,///2/1342,///2/1343,///2/1344,///2/1345,///2/1384,///2/1385,///2/1386,///2/1387,///2/1388,///2/1389,///2/1390,///2/1481,///2/1482,///2/1483,///2/1484,///2/1485,///2/1486,///2/1487,///2/1488,///2/1489,///2/1490,///2/1491,///2/1492,///2/1493,///2/1494,///2/1495,///2/1496,///2/1497,///2/1498", "num_stems": 3, "bridges": [ { "index": 1, "num_nts": 11, "nts_short": "GGCCGUUCUUA", "nts_long": "///2/1334,///2/1335,///2/1336,///2/1337,///2/1338,///2/1339,///2/1340,///2/1341,///2/1342,///2/1343,///2/1344" }, { "index": 2, "num_nts": 5, "nts_short": "GAGAC", "nts_long": "///2/1385,///2/1386,///2/1387,///2/1388,///2/1389" }, { "index": 3, "num_nts": 16, "nts_short": "CAAUAACAGGUCUGUG", "nts_long": "///2/1482,///2/1483,///2/1484,///2/1485,///2/1486,///2/1487,///2/1488,///2/1489,///2/1490,///2/1491,///2/1492,///2/1493,///2/1494,///2/1495,///2/1496,///2/1497" } ] }, { "index": 11, "type": "4-way junction", "bridging_nts": [ 7, 1, 3, 0 ], "stem_indices": [ 11, 12, 22, 25 ], "summary": "[4] 7 1 3 0 [2.98 2.432 2.106 2.355 2.357 2.405 2.409 2.431] 3 3 3 3", "num_nts": 19, "nts_short": "CAUUAAAUCGCCGUGACGG", "nts_long": "///2/98,///2/99,///2/100,///2/101,///2/102,///2/103,///2/104,///2/105,///2/106,///2/355,///2/356,///2/357,///2/405,///2/406,///2/407,///2/408,///2/409,///2/431,///2/432", "num_stems": 4, "bridges": [ { "index": 1, "num_nts": 7, "nts_short": "AUUAAAU", "nts_long": "///2/99,///2/100,///2/101,///2/102,///2/103,///2/104,///2/105" }, { "index": 2, "num_nts": 1, "nts_short": "C", "nts_long": "///2/356" }, { "index": 3, "num_nts": 3, "nts_short": "UGA", "nts_long": "///2/406,///2/407,///2/408" }, { "index": 4, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 12, "type": "5-way junction", "bridging_nts": [ 0, 0, 2, 3, 0 ], "stem_indices": [ -22, 40, 63, 40, -23 ], "summary": "[5] 0 0 2 3 0 [2.665 2.1162 2.666 2.1145 2.1146 2.1141 2.1144 2.667 2.671 2.1161] 1 2 2 2 1", "is_repeated": true, "num_nts": 15, "nts_short": "GUACGGAAUAAAAUC", "nts_long": "///2/665,///2/666,///2/1145,///2/1146,///2/1141,///2/1142,///2/1143,///2/1144,///2/667,///2/668,///2/669,///2/670,///2/671,///2/1161,///2/1162", "num_stems": 5, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 3, "num_nts": 2, "nts_short": "GA", "nts_long": "///2/1142,///2/1143" }, { "index": 4, "num_nts": 3, "nts_short": "AAA", "nts_long": "///2/668,///2/669,///2/670" }, { "index": 5, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 13, "type": "5-way junction", "bridging_nts": [ 0, 0, 2, 4, 0 ], "stem_indices": [ 36, 37, 39, 37, -19 ], "summary": "[5] 0 0 2 4 0 [2.599 2.637 2.600 2.622 2.623 2.618 2.621 2.601 2.606 2.636] 5 2 2 2 1", "is_repeated": true, "num_nts": 16, "nts_short": "AGCGCAGCGGCAAGCU", "nts_long": "///2/599,///2/600,///2/622,///2/623,///2/618,///2/619,///2/620,///2/621,///2/601,///2/602,///2/603,///2/604,///2/605,///2/606,///2/636,///2/637", "num_stems": 5, "bridges": [ { "index": 1, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 2, "num_nts": 0, "nts_short": "", "nts_long": "" }, { "index": 3, "num_nts": 2, "nts_short": "AG", "nts_long": "///2/619,///2/620" }, { "index": 4, "num_nts": 4, "nts_short": "GCAA", "nts_long": "///2/602,///2/603,///2/604,///2/605" }, { "index": 5, "num_nts": 0, "nts_short": "", "nts_long": "" } ] }, { "index": 14, "type": "5-way junction", "bridging_nts": [ 2, 6, 1, 1, 3 ], "stem_indices": [ 7, 8, 11, 27, -13 ], "summary": "[5] 2 6 1 1 3 [2.53 2.474 2.56 2.89 2.96 2.434 2.436 2.457 2.459 2.470] 3 2 3 2 1", "num_nts": 23, "nts_short": "CAUGCGAAUGGCGAGCACGGCAG", "nts_long": "///2/53,///2/54,///2/55,///2/56,///2/89,///2/90,///2/91,///2/92,///2/93,///2/94,///2/95,///2/96,///2/434,///2/435,///2/436,///2/457,///2/458,///2/459,///2/470,///2/471,///2/472,///2/473,///2/474", "num_stems": 5, "bridges": [ { "index": 1, "num_nts": 2, "nts_short": "AU", "nts_long": "///2/54,///2/55" }, { "index": 2, "num_nts": 6, "nts_short": "GAAUGG", "nts_long": "///2/90,///2/91,///2/92,///2/93,///2/94,///2/95" }, { "index": 3, "num_nts": 1, "nts_short": "A", "nts_long": "///2/435" }, { "index": 4, "num_nts": 1, "nts_short": "A", "nts_long": "///2/458" }, { "index": 5, "num_nts": 3, "nts_short": "GCA", "nts_long": "///2/471,///2/472,///2/473" } ] }, { "index": 15, "type": "5-way junction", "bridging_nts": [ 3, 5, 4, 2, 2 ], "stem_indices": [ 4, -2, 32, -17, 36 ], "summary": "[5] 3 5 4 2 2 [2.30 2.644 2.34 2.521 2.527 2.558 2.563 2.592 2.595 2.641] 6 1 3 1 5", "num_nts": 26, "nts_short": "CUUGUAAAUAACGGAAUGCCAUAUAG", "nts_long": "///2/30,///2/31,///2/32,///2/33,///2/34,///2/521,///2/522,///2/523,///2/524,///2/525,///2/526,///2/527,///2/558,///2/559,///2/560,///2/561,///2/562,///2/563,///2/592,///2/593,///2/594,///2/595,///2/641,///2/642,///2/643,///2/644", "num_stems": 5, "bridges": [ { "index": 1, "num_nts": 3, "nts_short": "UUG", "nts_long": "///2/31,///2/32,///2/33" }, { "index": 2, "num_nts": 5, "nts_short": "AAUAA", "nts_long": "///2/522,///2/523,///2/524,///2/525,///2/526" }, { "index": 3, "num_nts": 4, "nts_short": "GAAU", "nts_long": "///2/559,///2/560,///2/561,///2/562" }, { "index": 4, "num_nts": 2, "nts_short": "CA", "nts_long": "///2/593,///2/594" }, { "index": 5, "num_nts": 2, "nts_short": "UA", "nts_long": "///2/642,///2/643" } ] }, { "index": 16, "type": "5-way junction", "bridging_nts": [ 7, 2, 1, 2, 4 ], "stem_indices": [ 14, -8, 18, -10, -12 ], "summary": "[5] 7 2 1 2 4 [2.122 2.342 2.130 2.182 2.185 2.214 2.216 2.309 2.312 2.337] 2 1 4 1 1", "num_nts": 26, "nts_short": "GGUCGCUCGCGGGUGCGCCGCGACCC", "nts_long": "///2/122,///2/123,///2/124,///2/125,///2/126,///2/127,///2/128,///2/129,///2/130,///2/182,///2/183,///2/184,///2/185,///2/214,///2/215,///2/216,///2/309,///2/310,///2/311,///2/312,///2/337,///2/338,///2/339,///2/340,///2/341,///2/342", "num_stems": 5, "bridges": [ { "index": 1, "num_nts": 7, "nts_short": "GUCGCUC", "nts_long": "///2/123,///2/124,///2/125,///2/126,///2/127,///2/128,///2/129" }, { "index": 2, "num_nts": 2, "nts_short": "GG", "nts_long": "///2/183,///2/184" }, { "index": 3, "num_nts": 1, "nts_short": "G", "nts_long": "///2/215" }, { "index": 4, "num_nts": 2, "nts_short": "CC", "nts_long": "///2/310,///2/311" }, { "index": 5, "num_nts": 4, "nts_short": "GACC", "nts_long": "///2/338,///2/339,///2/340,///2/341" } ] }, { "index": 17, "type": "5-way junction", "bridging_nts": [ 15, 13, 5, 12, 31 ], "stem_indices": [ -35, 71, -36, -37, -38 ], "summary": "[5] 15 13 5 12 31 [2.1228 2.1530 2.1244 2.1255 2.1269 2.1271 2.1277 2.1320 2.1333 2.1498] 1 2 1 1 1", "num_nts": 86, "nts_short": "AGCCUGCGGCUUAAUUUGGGAAACCUCACCCGCCCGGACGGGUGGUGGUGCAUAUGCCCUUAGAUGUCCGGGGCUGCACGCGCGCU", "nts_long": "///2/1228,///2/1229,///2/1230,///2/1231,///2/1232,///2/1233,///2/1234,///2/1235,///2/1236,///2/1237,///2/1238,///2/1239,///2/1240,///2/1241,///2/1242,///2/1243,///2/1244,///2/1255,///2/1256,///2/1257,///2/1258,///2/1259,///2/1260,///2/1261,///2/1262,///2/1263,///2/1264,///2/1265,///2/1266,///2/1267,///2/1268,///2/1269,///2/1271,///2/1272,///2/1273,///2/1274,///2/1275,///2/1276,///2/1277,///2/1320,///2/1321,///2/1322,///2/1323,///2/1324,///2/1325,///2/1326,///2/1327,///2/1328,///2/1329,///2/1330,///2/1331,///2/1332,///2/1333,///2/1498,///2/1499,///2/1500,///2/1501,///2/1502,///2/1503,///2/1504,///2/1505,///2/1506,///2/1507,///2/1508,///2/1509,///2/1510,///2/1511,///2/1512,///2/1513,///2/1514,///2/1515,///2/1516,///2/1517,///2/1518,///2/1519,///2/1520,///2/1521,///2/1522,///2/1523,///2/1524,///2/1525,///2/1526,///2/1527,///2/1528,///2/1529,///2/1530", "num_stems": 5, "bridges": [ { "index": 1, "num_nts": 15, "nts_short": "GCCUGCGGCUUAAUU", "nts_long": "///2/1229,///2/1230,///2/1231,///2/1232,///2/1233,///2/1234,///2/1235,///2/1236,///2/1237,///2/1238,///2/1239,///2/1240,///2/1241,///2/1242,///2/1243" }, { "index": 2, "num_nts": 13, "nts_short": "GGAAACCUCACCC", "nts_long": "///2/1256,///2/1257,///2/1258,///2/1259,///2/1260,///2/1261,///2/1262,///2/1263,///2/1264,///2/1265,///2/1266,///2/1267,///2/1268" }, { "index": 3, "num_nts": 5, "nts_short": "CCGGA", "nts_long": "///2/1272,///2/1273,///2/1274,///2/1275,///2/1276" }, { "index": 4, "num_nts": 12, "nts_short": "GGUGGUGGUGCA", "nts_long": "///2/1321,///2/1322,///2/1323,///2/1324,///2/1325,///2/1326,///2/1327,///2/1328,///2/1329,///2/1330,///2/1331,///2/1332" }, { "index": 5, "num_nts": 31, "nts_short": "UGCCCUUAGAUGUCCGGGGCUGCACGCGCGC", "nts_long": "///2/1499,///2/1500,///2/1501,///2/1502,///2/1503,///2/1504,///2/1505,///2/1506,///2/1507,///2/1508,///2/1509,///2/1510,///2/1511,///2/1512,///2/1513,///2/1514,///2/1515,///2/1516,///2/1517,///2/1518,///2/1519,///2/1520,///2/1521,///2/1522,///2/1523,///2/1524,///2/1525,///2/1526,///2/1527,///2/1528,///2/1529" } ] } ], "num_ssSegments": 25, "ssSegments": [ { "index": 1, "num_nts": 3, "nts_short": "UAC", "nts_long": "///2/1,///2/2,///2/3" }, { "index": 2, "num_nts": 3, "nts_short": "ACU", "nts_long": "///2/141,///2/142,///2/143" }, { "index": 3, "num_nts": 6, "nts_short": "UGCCGA", "nts_long": "///2/176,///2/177,///2/178,///2/179,///2/180,///2/181" }, { "index": 4, "is_broken": true, "num_nts": 3, "nts_short": "AGU", "nts_long": "///2/224,///2/225,///2/287" }, { "index": 5, "num_nts": 2, "nts_short": "UA", "nts_long": "///2/296,///2/297" }, { "index": 6, "is_broken": true, "num_nts": 9, "nts_short": "ACGCCGGCG", "nts_long": "///2/318,///2/319,///2/320,///2/321,///2/322,///2/329,///2/330,///2/331,///2/332" }, { "index": 7, "num_nts": 2, "nts_short": "AA", "nts_long": "///2/654,///2/655" }, { "index": 8, "num_nts": 6, "nts_short": "UUGCUG", "nts_long": "///2/657,///2/658,///2/659,///2/660,///2/661,///2/662" }, { "index": 9, "num_nts": 1, "nts_short": "A", "nts_long": "///2/672" }, { "index": 10, "is_broken": true, "num_nts": 23, "nts_short": "GGAUCUCUCUCGGCCGAAGCGUU", "nts_long": "///2/683,///2/684,///2/685,///2/686,///2/687,///2/688,///2/746,///2/747,///2/748,///2/749,///2/750,///2/751,///2/752,///2/791,///2/792,///2/793,///2/794,///2/795,///2/796,///2/797,///2/798,///2/799,///2/800" }, { "index": 11, "num_nts": 1, "nts_short": "C", "nts_long": "///2/834" }, { "index": 12, "num_nts": 9, "nts_short": "AUGGAAUAG", "nts_long": "///2/865,///2/866,///2/867,///2/868,///2/869,///2/870,///2/871,///2/872,///2/873" }, { "index": 13, "num_nts": 9, "nts_short": "AUGAUUAAG", "nts_long": "///2/913,///2/914,///2/915,///2/916,///2/917,///2/918,///2/919,///2/920,///2/921" }, { "index": 14, "num_nts": 4, "nts_short": "GAAA", "nts_long": "///2/1033,///2/1034,///2/1035,///2/1036" }, { "index": 15, "num_nts": 6, "nts_short": "CAUAAA", "nts_long": "///2/1079,///2/1080,///2/1081,///2/1082,///2/1083,///2/1084" }, { "index": 16, "num_nts": 3, "nts_short": "GAU", "nts_long": "///2/1086,///2/1087,///2/1088" }, { "index": 17, "num_nts": 1, "nts_short": "G", "nts_long": "///2/1165" }, { "index": 18, "num_nts": 3, "nts_short": "AAA", "nts_long": "///2/1194,///2/1195,///2/1196" }, { "index": 19, "num_nts": 6, "nts_short": "UUACGC", "nts_long": "///2/1407,///2/1408,///2/1409,///2/1410,///2/1411,///2/1412" }, { "index": 20, "is_broken": true, "num_nts": 6, "nts_short": "ACCGGU", "nts_long": "///2/1414,///2/1415,///2/1416,///2/1424,///2/1425,///2/1426" }, { "index": 21, "is_broken": true, "num_nts": 7, "nts_short": "GGCGUAA", "nts_long": "///2/1428,///2/1429,///2/1430,///2/1431,///2/1432,///2/1438,///2/1439" }, { "index": 22, "num_nts": 2, "nts_short": "CA", "nts_long": "///2/1698,///2/1699" }, { "index": 23, "is_broken": true, "num_nts": 24, "nts_short": "CCCGCCGGGGUGCCCUGGCGGAGC", "nts_long": "///2/1751,///2/1752,///2/1753,///2/1754,///2/1755,///2/1756,///2/1757,///2/1758,///2/1759,///2/1760,///2/1761,///2/1771,///2/1772,///2/1773,///2/1774,///2/1775,///2/1776,///2/1777,///2/1778,///2/1779,///2/1780,///2/1781,///2/1782,///2/1783" }, { "index": 24, "num_nts": 2, "nts_short": "GU", "nts_long": "///2/1837,///2/1838" }, { "index": 25, "num_nts": 8, "nts_short": "GAUCAUUA", "nts_long": "///2/1862,///2/1863,///2/1864,///2/1865,///2/1866,///2/1867,///2/1868,///2/1869" } ], "num_Aminors": 50, "Aminors": [ { "index": 1, "type": "X", "desc_short": "A vs U-A (WC)", "desc_long": "///2/46 vs ///2/97,///2/433", "A_nt1": { "desc": "///2/46 vs ///2/97", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N7-O2'(hydroxyl)[2.88],N6(amino)-O2(carbonyl)[3.00]" }, "A_nt2": { "desc": "///2/46 vs ///2/433", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 2, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///2/50 vs ///2/49,///2/477", "A_nt1": { "desc": "///2/50 vs ///2/49", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///2/50 vs ///2/477", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "N7-N2(amino)[2.89],N6(amino)-N3[3.25]" } }, { "index": 3, "type": "II", "desc_short": "A vs G-C (WC)", "desc_long": "///2/60 vs ///2/316,///2/334", "A_nt1": { "desc": "///2/60 vs ///2/316", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.00],N3-O2'(hydroxyl)[2.59]" }, "A_nt2": { "desc": "///2/60 vs ///2/334", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 4, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///2/61 vs ///2/315,///2/335", "A_nt1": { "desc": "///2/61 vs ///2/315", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.55]" }, "A_nt2": { "desc": "///2/61 vs ///2/335", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[2.86],N3-N2(amino)[3.17]" } }, { "index": 5, "type": "X", "desc_short": "A vs U-A (WC)", "desc_long": "///2/99 vs ///2/97,///2/433", "A_nt1": { "desc": "///2/99 vs ///2/97", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///2/99 vs ///2/433", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "N6(amino)-N3[2.83],N1-O2'(hydroxyl)[2.85]" } }, { "index": 6, "type": "X", "desc_short": "A vs U-A (WC)", "desc_long": "///2/149 vs ///2/63,///2/85", "A_nt1": { "desc": "///2/149 vs ///2/63", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///2/149 vs ///2/85", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.02],N3-O2'(hydroxyl)[2.56]" } }, { "index": 7, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///2/158 vs ///2/462,///2/467", "A_nt1": { "desc": "///2/158 vs ///2/462", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///2/158 vs ///2/467", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N6(amino)-N3[3.46],N1-N2(amino)[3.24]" } }, { "index": 8, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///2/159 vs ///2/462,///2/467", "A_nt1": { "desc": "///2/159 vs ///2/462", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///2/159 vs ///2/467", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[2.55]" } }, { "index": 9, "type": "X", "desc_short": "A vs U-A (WC)", "desc_long": "///2/170 vs ///2/63,///2/85", "A_nt1": { "desc": "///2/170 vs ///2/63", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.74],N3-O2'(hydroxyl)[2.64]" }, "A_nt2": { "desc": "///2/170 vs ///2/85", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 10, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///2/171 vs ///2/62,///2/86", "A_nt1": { "desc": "///2/171 vs ///2/62", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N3-N2(amino)[3.28]" }, "A_nt2": { "desc": "///2/171 vs ///2/86", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[3.05],N1-O2'(hydroxyl)[2.49]" } }, { "index": 11, "type": "I", "desc_short": "A vs A-U (WC)", "desc_long": "///2/401 vs ///2/364,///2/396", "A_nt1": { "desc": "///2/401 vs ///2/364", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[2.70]" }, "A_nt2": { "desc": "///2/401 vs ///2/396", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.63]" } }, { "index": 12, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///2/473 vs ///2/96,///2/434", "A_nt1": { "desc": "///2/473 vs ///2/96", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.95],O2'(hydroxyl)-O2(carbonyl)[2.34]" }, "A_nt2": { "desc": "///2/473 vs ///2/434", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[2.82],N3-N2(amino)[3.00]" } }, { "index": 13, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///2/493 vs ///2/490,///2/510", "A_nt1": { "desc": "///2/493 vs ///2/490", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///2/493 vs ///2/510", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "N6(amino)-N3[3.15],N1-O2'(hydroxyl)[2.85]" } }, { "index": 14, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///2/493 vs ///2/491,///2/509", "A_nt1": { "desc": "///2/493 vs ///2/491", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N7-O2'(hydroxyl)[2.85],N6(amino)-O2(carbonyl)[2.61]" }, "A_nt2": { "desc": "///2/493 vs ///2/509", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N6(amino)*N2(amino)[2.89]" } }, { "index": 15, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///2/574 vs ///2/490,///2/510", "A_nt1": { "desc": "///2/574 vs ///2/490", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "N6(amino)-O2(carbonyl)[2.97],N1-O2'(hydroxyl)[2.83]" }, "A_nt2": { "desc": "///2/574 vs ///2/510", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N6(amino)*N2(amino)[3.08]" } }, { "index": 16, "type": "X", "desc_short": "A vs A-U (WC)", "desc_long": "///2/575 vs ///2/489,///2/511", "A_nt1": { "desc": "///2/575 vs ///2/489", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///2/575 vs ///2/511", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[2.92]" } }, { "index": 17, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///2/605 vs ///2/598,///2/638", "A_nt1": { "desc": "///2/605 vs ///2/598", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[2.62],N3-N2(amino)[3.09]" }, "A_nt2": { "desc": "///2/605 vs ///2/638", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.72],O2'(hydroxyl)-O2(carbonyl)[3.35]" } }, { "index": 18, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///2/668 vs ///2/14,///2/1197", "A_nt1": { "desc": "///2/668 vs ///2/14", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[2.51]" }, "A_nt2": { "desc": "///2/668 vs ///2/1197", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.94],N3-N2(amino)[3.27]" } }, { "index": 19, "type": "II", "desc_short": "A vs C-G (WC)", "desc_long": "///2/669 vs ///2/663,///2/1164", "A_nt1": { "desc": "///2/669 vs ///2/663", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///2/669 vs ///2/1164", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N3-O2'(hydroxyl)[2.49]" } }, { "index": 20, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///2/811 vs ///2/411,///2/429", "A_nt1": { "desc": "///2/811 vs ///2/411", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N6(amino)*N2(amino)[3.41]" }, "A_nt2": { "desc": "///2/811 vs ///2/429", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "N6(amino)-O2(carbonyl)[3.05],N1-O2'(hydroxyl)[2.42]" } }, { "index": 21, "type": "II", "desc_short": "A vs C-A (~Wobble)", "desc_long": "///2/825 vs ///2/35,///2/520", "A_nt1": { "desc": "///2/825 vs ///2/35", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///2/825 vs ///2/520", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.92],N3-O2'(hydroxyl)[2.54]" } }, { "index": 22, "type": "X", "desc_short": "A vs U-A (WC)", "desc_long": "///2/826 vs ///2/36,///2/519", "A_nt1": { "desc": "///2/826 vs ///2/36", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[3.01]" }, "A_nt2": { "desc": "///2/826 vs ///2/519", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.05]" } }, { "index": 23, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///2/854 vs ///2/108,///2/353", "A_nt1": { "desc": "///2/854 vs ///2/108", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N3-N2(amino)[3.54]" }, "A_nt2": { "desc": "///2/854 vs ///2/353", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.46]" } }, { "index": 24, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///2/862 vs ///2/803,///2/860", "A_nt1": { "desc": "///2/862 vs ///2/803", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N6(amino)-O2(carbonyl)[2.99]" }, "A_nt2": { "desc": "///2/862 vs ///2/860", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 25, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///2/963 vs ///2/1054,///2/1064", "A_nt1": { "desc": "///2/963 vs ///2/1054", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N1-N2(amino)[3.42]" }, "A_nt2": { "desc": "///2/963 vs ///2/1064", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 26, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///2/964 vs ///2/1053,///2/1065", "A_nt1": { "desc": "///2/964 vs ///2/1053", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///2/964 vs ///2/1065", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[3.28],N1-O2'(hydroxyl)[2.87]" } }, { "index": 27, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///2/972 vs ///2/956,///2/967", "A_nt1": { "desc": "///2/972 vs ///2/956", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[3.04],N3-N2(amino)[3.27]" }, "A_nt2": { "desc": "///2/972 vs ///2/967", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.40]" } }, { "index": 28, "type": "II", "desc_short": "A vs C-A (~Wobble)", "desc_long": "///2/996 vs ///2/674,///2/1031", "A_nt1": { "desc": "///2/996 vs ///2/674", "face_type": "-", "hbonds_num": 3, "hbonds_desc": "O2'(hydroxyl)-O3'[3.18],O2'(hydroxyl)-O2'(hydroxyl)[2.50],N3-O2'(hydroxyl)[3.18]" }, "A_nt2": { "desc": "///2/996 vs ///2/1031", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 29, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///2/997 vs ///2/673,///2/1032", "A_nt1": { "desc": "///2/997 vs ///2/673", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.39],N3-N2(amino)[3.08]" }, "A_nt2": { "desc": "///2/997 vs ///2/1032", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[2.62]" } }, { "index": 30, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///2/1034 vs ///2/1842,///2/1857", "A_nt1": { "desc": "///2/1034 vs ///2/1842", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///2/1034 vs ///2/1857", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N3-O2'(hydroxyl)[2.89]" } }, { "index": 31, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///2/1035 vs ///2/1843,///2/1856", "A_nt1": { "desc": "///2/1035 vs ///2/1843", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N3-N2(amino)[3.09]" }, "A_nt2": { "desc": "///2/1035 vs ///2/1856", "face_type": "-", "hbonds_num": 3, "hbonds_desc": "O3'-O2'(hydroxyl)[2.75],O2'(hydroxyl)-O2'(hydroxyl)[2.83],O2'(hydroxyl)-O2(carbonyl)[2.81]" } }, { "index": 32, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///2/1143 vs ///2/13,///2/1198", "A_nt1": { "desc": "///2/1143 vs ///2/13", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.91]" }, "A_nt2": { "desc": "///2/1143 vs ///2/1198", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[2.89],N3-N2(amino)[2.87]" } }, { "index": 33, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///2/1150 vs ///2/1141,///2/1146", "A_nt1": { "desc": "///2/1150 vs ///2/1141", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///2/1150 vs ///2/1146", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[3.30],N1-O2'(hydroxyl)[2.43]" } }, { "index": 34, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///2/1181 vs ///2/1037,///2/1078", "A_nt1": { "desc": "///2/1181 vs ///2/1037", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N1-N2(amino)[2.89]" }, "A_nt2": { "desc": "///2/1181 vs ///2/1078", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 35, "type": "X", "desc_short": "A vs U-A (WC)", "desc_long": "///2/1190 vs ///2/1714,///2/1819", "A_nt1": { "desc": "///2/1190 vs ///2/1714", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.89],N3-O2'(hydroxyl)[2.88]" }, "A_nt2": { "desc": "///2/1190 vs ///2/1819", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 36, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///2/1194 vs ///2/7,///2/17", "A_nt1": { "desc": "///2/1194 vs ///2/7", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///2/1194 vs ///2/17", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[3.02],N1-O2'(hydroxyl)[2.35]" } }, { "index": 37, "type": "I", "desc_short": "A vs A-A (--)", "desc_long": "///2/1357 vs ///2/11,///2/1200", "A_nt1": { "desc": "///2/1357 vs ///2/11", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.86],O2'(hydroxyl)-N3[2.75]" }, "A_nt2": { "desc": "///2/1357 vs ///2/1200", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[2.71]" } }, { "index": 38, "type": "I", "desc_short": "A vs G-U (Wobble)", "desc_long": "///2/1378 vs ///2/1351,///2/1360", "A_nt1": { "desc": "///2/1378 vs ///2/1351", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[2.47],N3-N2(amino)[3.39]" }, "A_nt2": { "desc": "///2/1378 vs ///2/1360", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 39, "type": "X", "desc_short": "A vs A-U (--)", "desc_long": "///2/1402 vs ///2/1401,///2/1445", "A_nt1": { "desc": "///2/1402 vs ///2/1401", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "OP2-O2'(hydroxyl)[2.79]" }, "A_nt2": { "desc": "///2/1402 vs ///2/1445", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 40, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///2/1465 vs ///2/1366,///2/1373", "A_nt1": { "desc": "///2/1465 vs ///2/1366", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[2.96],N3-N2(amino)[3.02]" }, "A_nt2": { "desc": "///2/1465 vs ///2/1373", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.64],O2'(hydroxyl)-O2(carbonyl)[2.92]" } }, { "index": 41, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///2/1533 vs ///2/1536,///2/1597", "A_nt1": { "desc": "///2/1533 vs ///2/1536", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N3-O2'(hydroxyl)[3.53]" }, "A_nt2": { "desc": "///2/1533 vs ///2/1597", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 42, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///2/1537 vs ///2/1536,///2/1597", "A_nt1": { "desc": "///2/1537 vs ///2/1536", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///2/1537 vs ///2/1597", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N6(amino)-O2(carbonyl)[2.27]" } }, { "index": 43, "type": "X", "desc_short": "A vs G-C (WC)", "desc_long": "///2/1545 vs ///2/1654,///2/1670", "A_nt1": { "desc": "///2/1545 vs ///2/1654", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N6(amino)-O2'(hydroxyl)[3.49],N1-N2(amino)[3.44]" }, "A_nt2": { "desc": "///2/1545 vs ///2/1670", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 44, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///2/1569 vs ///2/1613,///2/1626", "A_nt1": { "desc": "///2/1569 vs ///2/1613", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[3.44],N3-N2(amino)[3.19]" }, "A_nt2": { "desc": "///2/1569 vs ///2/1626", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" } }, { "index": 45, "type": "X", "desc_short": "A vs C-G (WC)", "desc_long": "///2/1579 vs ///2/1558,///2/1577", "A_nt1": { "desc": "///2/1579 vs ///2/1558", "face_type": "+", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///2/1579 vs ///2/1577", "face_type": "-", "hbonds_num": 1, "hbonds_desc": "N3-O2'(hydroxyl)[2.59]" } }, { "index": 46, "type": "X", "desc_short": "A vs U-G (Wobble)", "desc_long": "///2/1589 vs ///2/1653,///2/1671", "A_nt1": { "desc": "///2/1589 vs ///2/1653", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///2/1589 vs ///2/1671", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-N2(amino)[3.03]" } }, { "index": 47, "type": "I", "desc_short": "A vs G-C (WC)", "desc_long": "///2/1699 vs ///2/1203,///2/1696", "A_nt1": { "desc": "///2/1699 vs ///2/1203", "face_type": "+", "hbonds_num": 2, "hbonds_desc": "N1-O2'(hydroxyl)[2.61],N3-N2(amino)[2.98]" }, "A_nt2": { "desc": "///2/1699 vs ///2/1696", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[2.93],O2'(hydroxyl)-O2(carbonyl)[2.98]" } }, { "index": 48, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///2/1834 vs ///2/1205,///2/1693", "A_nt1": { "desc": "///2/1834 vs ///2/1205", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[2.71]" }, "A_nt2": { "desc": "///2/1834 vs ///2/1693", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O5'-O2'(hydroxyl)[2.79],N3-N2(amino)[3.16]" } }, { "index": 49, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///2/1850 vs ///2/1705,///2/1829", "A_nt1": { "desc": "///2/1850 vs ///2/1705", "face_type": "-", "hbonds_num": 0, "hbonds_desc": "" }, "A_nt2": { "desc": "///2/1850 vs ///2/1829", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N1-O2'(hydroxyl)[3.04]" } }, { "index": 50, "type": "I", "desc_short": "A vs C-G (WC)", "desc_long": "///2/1851 vs ///2/1705,///2/1829", "A_nt1": { "desc": "///2/1851 vs ///2/1705", "face_type": "-", "hbonds_num": 2, "hbonds_desc": "O2'(hydroxyl)-O2'(hydroxyl)[3.07],O2'(hydroxyl)-O2(carbonyl)[2.58]" }, "A_nt2": { "desc": "///2/1851 vs ///2/1829", "face_type": "+", "hbonds_num": 1, "hbonds_desc": "N3-N2(amino)[3.19]" } } ], "num_riboseZippers": 12, "riboseZippers": [ { "index": 1, "num_nts": 4, "nts_short": "AUGA", "nts_long": "///2/11,///2/12,///2/1356,///2/1357" }, { "index": 2, "num_nts": 4, "nts_short": "AACG", "nts_long": "///2/60,///2/61,///2/315,///2/316" }, { "index": 3, "num_nts": 4, "nts_short": "AAAA", "nts_long": "///2/84,///2/85,///2/149,///2/150" }, { "index": 4, "num_nts": 4, "nts_short": "GCAG", "nts_long": "///2/95,///2/96,///2/473,///2/474" }, { "index": 5, "num_nts": 4, "nts_short": "GUCC", "nts_long": "///2/114,///2/115,///2/381,///2/382" }, { "index": 6, "num_nts": 4, "nts_short": "UAAG", "nts_long": "///2/454,///2/455,///2/1735,///2/1736" }, { "index": 7, "num_nts": 4, "nts_short": "AAAA", "nts_long": "///2/519,///2/520,///2/825,///2/826" }, { "index": 8, "num_nts": 4, "nts_short": "GCAA", "nts_long": "///2/673,///2/674,///2/996,///2/997" }, { "index": 9, "num_nts": 4, "nts_short": "AUCG", "nts_long": "///2/964,///2/965,///2/1053,///2/1054" }, { "index": 10, "num_nts": 4, "nts_short": "UACG", "nts_long": "///2/1081,///2/1082,///2/1842,///2/1843" }, { "index": 11, "num_nts": 4, "nts_short": "AGCG", "nts_long": "///2/1545,///2/1546,///2/1670,///2/1671" }, { "index": 12, "num_nts": 4, "nts_short": "CGAA", "nts_long": "///2/1705,///2/1706,///2/1850,///2/1851" } ], "num_Kturns": 1, "Kturns": [ { "index": 1, "type": "Normal k-turn", "iloop_index": 52, "bounding_stems": [ 54, 53 ], "Cstem_index": 54, "NCstem_index": 53, "Cstem_pair": "C-G (///2/967,///2/956) WC", "NCstem_pair": "C-G (///2/974,///2/952) WC", "GA_pair": "G-A (///2/971,///2/955) Sheared", "bending_angle": 53.597, "strand1": { "num_nts": 16, "nts_short": "UCUUGGACCGGCGCAA", "nts_long": "///2/966,///2/967,///2/968,///2/969,///2/970,///2/971,///2/972,///2/973,///2/974,///2/975,///2/976,///2/977,///2/978,///2/979,///2/980,///2/981" }, "strand2": { "num_nts": 13, "nts_short": "UUGCGCCGCUAGA", "nts_long": "///2/945,///2/946,///2/947,///2/948,///2/949,///2/950,///2/951,///2/952,///2/953,///2/954,///2/955,///2/956,///2/957" } } ], "num_splayUnits": 166, "splayUnits": [ { "index": 1, "num_nts": 3, "nts_short": "UAC", "nts_long": "///2/1,///2/2,///2/3" }, { "index": 2, "num_nts": 2, "nts_short": "UU", "nts_long": "///2/8,///2/9" }, { "index": 3, "num_nts": 2, "nts_short": "UG", "nts_long": "///2/32,///2/33" }, { "index": 4, "num_nts": 3, "nts_short": "AGA", "nts_long": "///2/40,///2/41,///2/42" }, { "index": 5, "num_nts": 3, "nts_short": "AAG", "nts_long": "///2/45,///2/46,///2/47" }, { "index": 6, "num_nts": 2, "nts_short": "AU", "nts_long": "///2/54,///2/55" }, { "index": 7, "num_nts": 2, "nts_short": "AG", "nts_long": "///2/61,///2/62" }, { "index": 8, "num_nts": 4, "nts_short": "ACGC", "nts_long": "///2/64,///2/65,///2/66,///2/67" }, { "index": 9, "num_nts": 3, "nts_short": "CGG", "nts_long": "///2/73,///2/74,///2/75" }, { "index": 10, "num_nts": 2, "nts_short": "UA", "nts_long": "///2/76,///2/77" }, { "index": 11, "num_nts": 2, "nts_short": "CA", "nts_long": "///2/78,///2/79" }, { "index": 12, "num_nts": 2, "nts_short": "AU", "nts_long": "///2/92,///2/93" }, { "index": 13, "num_nts": 3, "nts_short": "UGG", "nts_long": "///2/112,///2/113,///2/114" }, { "index": 14, "num_nts": 2, "nts_short": "CC", "nts_long": "///2/117,///2/118" }, { "index": 15, "num_nts": 3, "nts_short": "CGC", "nts_long": "///2/125,///2/126,///2/127" }, { "index": 16, "num_nts": 2, "nts_short": "UC", "nts_long": "///2/128,///2/129" }, { "index": 17, "num_nts": 3, "nts_short": "ACU", "nts_long": "///2/141,///2/142,///2/143" }, { "index": 18, "num_nts": 3, "nts_short": "UUC", "nts_long": "///2/160,///2/161,///2/162" }, { "index": 19, "num_nts": 3, "nts_short": "AUA", "nts_long": "///2/171,///2/172,///2/173" }, { "index": 20, "num_nts": 2, "nts_short": "UU", "nts_long": "///2/197,///2/198" }, { "index": 21, "num_nts": 3, "nts_short": "CGC", "nts_long": "///2/199,///2/200,///2/201" }, { "index": 22, "num_nts": 2, "nts_short": "UG", "nts_long": "///2/214,///2/215" }, { "index": 23, "num_nts": 3, "nts_short": "CUC", "nts_long": "///2/293,///2/294,///2/295" }, { "index": 24, "num_nts": 6, "nts_short": "CUCGGG", "nts_long": "///2/304,///2/305,///2/306,///2/307,///2/308,///2/309" }, { "index": 25, "num_nts": 4, "nts_short": "CGAU", "nts_long": "///2/311,///2/312,///2/313,///2/314" }, { "index": 26, "num_nts": 3, "nts_short": "AUU", "nts_long": "///2/343,///2/344,///2/345" }, { "index": 27, "num_nts": 3, "nts_short": "AUC", "nts_long": "///2/360,///2/361,///2/362" }, { "index": 28, "num_nts": 2, "nts_short": "UU", "nts_long": "///2/367,///2/368" }, { "index": 29, "num_nts": 2, "nts_short": "CG", "nts_long": "///2/369,///2/370" }, { "index": 30, "num_nts": 2, "nts_short": "UG", "nts_long": "///2/384,///2/385" }, { "index": 31, "num_nts": 3, "nts_short": "ACC", "nts_long": "///2/398,///2/399,///2/400" }, { "index": 32, "num_nts": 3, "nts_short": "UGA", "nts_long": "///2/406,///2/407,///2/408" }, { "index": 33, "num_nts": 2, "nts_short": "CA", "nts_long": "///2/417,///2/418" }, { "index": 34, "num_nts": 2, "nts_short": "GA", "nts_long": "///2/425,///2/426" }, { "index": 35, "num_nts": 3, "nts_short": "UUC", "nts_long": "///2/427,///2/428,///2/429" }, { "index": 36, "num_nts": 2, "nts_short": "AG", "nts_long": "///2/435,///2/436" }, { "index": 37, "num_nts": 2, "nts_short": "AA", "nts_long": "///2/447,///2/448" }, { "index": 38, "num_nts": 3, "nts_short": "CGG", "nts_long": "///2/450,///2/451,///2/452" }, { "index": 39, "num_nts": 3, "nts_short": "CAA", "nts_long": "///2/463,///2/464,///2/465" }, { "index": 40, "num_nts": 4, "nts_short": "GCAG", "nts_long": "///2/471,///2/472,///2/473,///2/474" }, { "index": 41, "num_nts": 2, "nts_short": "AA", "nts_long": "///2/485,///2/486" }, { "index": 42, "num_nts": 3, "nts_short": "UUA", "nts_long": "///2/487,///2/488,///2/489" }, { "index": 43, "num_nts": 2, "nts_short": "GA", "nts_long": "///2/499,///2/500" }, { "index": 44, "num_nts": 2, "nts_short": "CC", "nts_long": "///2/501,///2/502" }, { "index": 45, "num_nts": 2, "nts_short": "CG", "nts_long": "///2/503,///2/504" }, { "index": 46, "num_nts": 3, "nts_short": "GGA", "nts_long": "///2/506,///2/507,///2/508" }, { "index": 47, "num_nts": 3, "nts_short": "GAC", "nts_long": "///2/515,///2/516,///2/517" }, { "index": 48, "num_nts": 2, "nts_short": "UA", "nts_long": "///2/524,///2/525" }, { "index": 49, "num_nts": 2, "nts_short": "CU", "nts_long": "///2/537,///2/538" }, { "index": 50, "num_nts": 2, "nts_short": "UU", "nts_long": "///2/540,///2/541" }, { "index": 51, "num_nts": 2, "nts_short": "UC", "nts_long": "///2/542,///2/543" }, { "index": 52, "num_nts": 3, "nts_short": "GGC", "nts_long": "///2/546,///2/547,///2/548" }, { "index": 53, "num_nts": 3, "nts_short": "AAU", "nts_long": "///2/554,///2/555,///2/556" }, { "index": 54, "num_nts": 7, "nts_short": "GGAUCCA", "nts_long": "///2/588,///2/589,///2/590,///2/591,///2/592,///2/593,///2/594" }, { "index": 55, "num_nts": 2, "nts_short": "AG", "nts_long": "///2/599,///2/600" }, { "index": 56, "num_nts": 3, "nts_short": "GUC", "nts_long": "///2/606,///2/607,///2/608" }, { "index": 57, "num_nts": 3, "nts_short": "GCC", "nts_long": "///2/613,///2/614,///2/615" }, { "index": 58, "num_nts": 2, "nts_short": "AG", "nts_long": "///2/619,///2/620" }, { "index": 59, "num_nts": 5, "nts_short": "GUAAU", "nts_long": "///2/626,///2/627,///2/628,///2/629,///2/630" }, { "index": 60, "num_nts": 2, "nts_short": "UC", "nts_long": "///2/631,///2/632" }, { "index": 61, "num_nts": 4, "nts_short": "AGUU", "nts_long": "///2/655,///2/656,///2/657,///2/658" }, { "index": 62, "num_nts": 2, "nts_short": "GC", "nts_long": "///2/659,///2/660" }, { "index": 63, "num_nts": 2, "nts_short": "GC", "nts_long": "///2/662,///2/663" }, { "index": 64, "num_nts": 2, "nts_short": "GU", "nts_long": "///2/665,///2/666" }, { "index": 65, "num_nts": 2, 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"residue_pair": "aa:aa" }, { "index": 7709, "atom1_serNum": 74738, "atom2_serNum": 74764, "donAcc_type": "standard", "distance": 2.932, "atom1_id": "///n/168/O", "atom2_id": "///n/172/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 7710, "atom1_serNum": 74742, "atom2_serNum": 74773, "donAcc_type": "standard", "distance": 2.853, "atom1_id": "///n/169/O", "atom2_id": "///n/173/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 7711, "atom1_serNum": 74749, "atom2_serNum": 74781, "donAcc_type": "standard", "distance": 2.917, "atom1_id": "///n/170/O", "atom2_id": "///n/174/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 7712, "atom1_serNum": 74756, "atom2_serNum": 74789, "donAcc_type": "standard", "distance": 2.909, "atom1_id": "///n/171/O", "atom2_id": "///n/175/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 7713, "atom1_serNum": 74762, "atom2_serNum": 74772, "donAcc_type": "standard", "distance": 2.741, "atom1_id": "///n/171/NH1", "atom2_id": "///n/172/OE2", "atom_pair": "N:O", "residue_pair": "aa:aa" }, { "index": 7714, "atom1_serNum": 74767, "atom2_serNum": 74800, "donAcc_type": "standard", "distance": 2.998, "atom1_id": "///n/172/O", "atom2_id": "///n/176/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 7715, "atom1_serNum": 74772, "atom2_serNum": 74798, "donAcc_type": "standard", "distance": 2.625, "atom1_id": "///n/172/OE2", "atom2_id": "///n/175/NH1", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 7716, "atom1_serNum": 74776, "atom2_serNum": 74809, "donAcc_type": "standard", "distance": 2.865, "atom1_id": "///n/173/O", "atom2_id": "///n/177/N", "atom_pair": "O:N", "residue_pair": "aa:aa" }, { "index": 7717, "atom1_serNum": 74784, "atom2_serNum": 74823, "donAcc_type": "questionable", "distance": 2.687, "atom1_id": "///n/174/O", "atom2_id": "///n/178/OD1", "atom_pair": "O:O", "residue_pair": "aa:aa" } ], "refCoords": { "purine": [ " 12 ATOMS, 12 BONDS", " 1 N -2.2500 5.0000 0.4000", " 2 N -2.2500 -0.5000 0.4000", " 3 N -2.2500 -0.5000 -0.4000", " 4 N -2.2500 5.0000 -0.4000", " 5 C 1.2500 5.0000 0.4000", " 6 C 1.2500 -0.5000 0.4000", " 7 C 1.2500 -0.5000 -0.4000", " 8 C 1.2500 5.0000 -0.4000", " 9 C -2.2500 5.0000 0.4000", " 10 C -2.2500 -0.5000 0.4000", " 11 C -2.2500 -0.5000 -0.4000", " 12 C -2.2500 5.0000 -0.4000", " 1 1 2", " 2 2 3", " 3 3 4", " 4 4 1", " 5 5 6", " 6 6 7", " 7 7 8", " 8 5 8", " 9 9 5", " 10 10 6", " 11 11 7", " 12 12 8" ], "pyrimidine": [ " 12 ATOMS, 12 BONDS", " 1 N -2.2500 5.0000 0.4000", " 2 N -2.2500 1.0000 0.4000", " 3 N -2.2500 1.0000 -0.4000", " 4 N -2.2500 5.0000 -0.4000", " 5 C 1.2500 5.0000 0.4000", " 6 C 1.2500 1.0000 0.4000", " 7 C 1.2500 1.0000 -0.4000", " 8 C 1.2500 5.0000 -0.4000", " 9 C -2.2500 5.0000 0.4000", " 10 C -2.2500 1.0000 0.4000", " 11 C -2.2500 1.0000 -0.4000", " 12 C -2.2500 5.0000 -0.4000", " 1 1 2", " 2 2 3", " 3 3 4", " 4 4 1", " 5 5 6", " 6 6 7", " 7 7 8", " 8 5 8", " 9 9 5", " 10 10 6", " 11 11 7", " 12 12 8" ], "wc_pair": [ " 12 ATOMS, 12 BONDS", " 1 N -2.2500 5.0000 0.4000", " 2 N -2.2500 -5.0000 0.4000", " 3 N -2.2500 -5.0000 -0.4000", " 4 N -2.2500 5.0000 -0.4000", " 5 C 2.2500 5.0000 0.4000", " 6 C 2.2500 -5.0000 0.4000", " 7 C 2.2500 -5.0000 -0.4000", " 8 C 2.2500 5.0000 -0.4000", " 9 C -2.2500 5.0000 0.4000", " 10 C -2.2500 -5.0000 0.4000", " 11 C -2.2500 -5.0000 -0.4000", " 12 C -2.2500 5.0000 -0.4000", " 1 1 2", " 2 2 3", " 3 3 4", " 4 4 1", " 5 5 6", " 6 6 7", " 7 7 8", " 8 5 8", " 9 9 5", " 10 10 6", " 11 11 7", " 12 12 8" ] }, "metadata": { "license": "http://innovation.columbia.edu/technologies/CU20391", "url": "http://x3dna.org/", "url_alt": "http://home.x3dna.org/", "forum": "http://forum.x3dna.org/", "citation": "Lu et al. (2015). 'DSSR: an integrated software tool for dissecting the spatial structure of RNA.' Nucleic Acids Res., 43(21):e142 [doi:10.1093/nar/gkv716].", "str_id": "9kmw", "num_aaChains": 35, "aaChains": "A=213,B=213,C=218,D=225,E=262,F=189,G=230,H=186,I=205,J=180,K=97,L=151,M=121,N=149,O=135,P=126,Q=138,R=132,S=143,T=144,U=101,V=82,W=129,X=141,Y=124,Z=72,a=99,b=82,c=62,d=55,e=56,f=74,g=314,h=22,n=30", "num_naChains": 1, "naChains": "2=1671", "num_atoms": 74798, "num_waters": 0, "num_notes": 52, "notes": [ { "Aminors": "A-minor interactions (including types I and II)" }, { "Cstem_index": "stem index of the 'Canonical' helix in k-turn" }, { "Cstem_pair": "Cstem bp delineating the k-turn internal loop" }, { "Dp": "perpendicular distance of the 3' P atom to the glycosidic bond" }, { "GA_pair": "sheared G-A pair in k-turn" }, { "HtypePknot": "H-type pseudoknot" }, { "Kturn": "kink-turn (k-turn)" }, { "LW": "Leontis-Westhof" }, { "NCstem_index": "stem index of the 'Non-Canonical' helix in k-turn" }, { "NCstem_pair": "NCstem bp delineating the k-turn internal loop" }, { "Uturn": "U-turn of the UNR- or GNRA-type" }, { "aa": "amino acid" }, { "atom_pair": "symbols of the two atoms involved in an H-bond" }, { "auxfiles": "auxiliary files" }, { "glyco_bond": "conformation of base related to sugar (syn or anti)" }, { "bb_type": "backbone conformation, BI or BII" }, { "bending_angle": "angle between two helical axes" }, { "bp": "base pair" }, { "bseq": "base sequence in one-letter code" }, { "bulge": "bulge loop" }, { "coaxStacks": "coaxial stacking of stems within a helix" }, { "dbn": "dot bracket notation" }, { "desc": "description" }, { "donAcc_type": "donor/acceptor type of the atom pair in an H-bond" }, { "epsilon_zeta": "difference between epsilon and zeta torsion angles" }, { "hairpin": "hairpin loop" }, { "hbond": "hydrogen bond (H-bond)" }, { "helix": "defined by base-stacking interactions, regardless of bp type and backbone connectivity" }, { "id": "identifier" }, { "iloop": "internal loop" }, { "index": "serial number" }, { "isoCanonPairs": "isolated canonical pairs" }, { "junction": "(multi-branched) junction loop" }, { "kissingLoop": "kissing loop" }, { "multiplet": "3+ bases in a coplanar geometry" }, { "na": "nucleic acid" }, { "nonPair": "two nts not forming a pair, but with H-bonding/stacking interactions" }, { "nonStack": "nucleotide not involved in stacking interactions" }, { "nt": "nucleotide" }, { "num": "number" }, { "oArea": "overlap areas between two bases, including exocyclic atoms" }, { "oArea_ring": "overlap areas between two bases, including only ring atoms" }, { "phosContacts": "H-bonding and atom-capping interactions involving a phosphate" }, { "residue_pair": "types of the two residues involved in an H-bond" }, { "rmsd": "root-mean-squares deviation" }, { "serNum": "serial number" }, { "ssSegments": "single-stranded segments not involved in loops" }, { "ssZp": "Z-coordinate of the 3' phosphorus atom with reference to the 5' base plane" }, { "sstr": "secondary structure in dbn" }, { "stem": "helix consisting of only canonical pairs, with a continuous backbone" }, { "str_id": "structure identifier, derived from inpfile with extension removed" }, { "vert_dist": "vertical distance from an atom to a base plane" } ], "num_auxfiles": 21, "auxfiles": [ { "index": 1, "name": "dssr-pairs.pdb", "desc": "an ensemble of base pairs" }, { "index": 2, "name": "dssr-multiplets.pdb", "desc": "an ensemble of multiplets" }, { "index": 3, "name": "dssr-stems.pdb", "desc": "an ensemble of stems" }, { "index": 4, "name": "dssr-helices.pdb", "desc": "an ensemble of helices (coaxial stacking)" }, { "index": 5, "name": "dssr-hairpins.pdb", "desc": "an ensemble of hairpin loops" }, { "index": 6, "name": "dssr-bulges.pdb", "desc": "an ensemble of bulges" }, { "index": 7, "name": "dssr-iloops.pdb", "desc": "an ensemble of internal loops" }, { "index": 8, "name": "dssr-junctions.pdb", "desc": "an ensemble of junctions (multi-branch)" }, { "index": 9, "name": "dssr-2ndstrs.bpseq", "desc": "secondary structure in bpseq format" }, { "index": 10, "name": "dssr-2ndstrs.ct", "desc": "secondary structure in connectivity table format" }, { "index": 11, "name": "dssr-2ndstrs.dbn", "desc": "secondary structure in dot-bracket notation" }, { "index": 12, "name": "dssr-torsions.txt", "desc": "backbone torsion angles and suite names" }, { "index": 13, "name": "dssr-splays.pdb", "desc": "an ensemble of splayed-apart units" }, { "index": 14, "name": "dssr-Aminors.pdb", "desc": "an ensemble of A minor motifs (types I and II)" }, { "index": 15, "name": "dssr-Kturns.pdb", "desc": "an ensemble of kink-turn motifs" }, { "index": 16, "name": "dssr-stacks.pdb", "desc": "an ensemble of base stacks" }, { "index": 17, "name": "dssr-atom2bases.pdb", "desc": "an ensemble of atom-base stacking interactions" }, { "index": 18, "name": "dssr-rotmat.txt", "desc": "position vector and rotation matrix" }, { "index": 19, "name": "dssr-viewV.pdb", "desc": "vertical view of the principal moment of inertia" }, { "index": 20, "name": "dssr-viewH.pdb", "desc": "horizontal view of the principal moment of inertia" }, { "index": 21, "name": "dssr-viewT.pdb", "desc": "top view of the principal moment of inertia" } ], "time_used": "999" } }